Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to ob...Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to obtain target cultivars with desirable traits.Sweet potato[Ipomoea batatas(L.)Lam]is widely considered the world’s most important crop,with great diversity in morphological and phenotypic traits.The genetic diversity of 20 sweet potato germplasms originating from Bangladesh,CIP,Philippines,Taiwan,and Malaysia were compared,which was accomplished by genetic diversity analysis by exploring 20 microsatellite DNA markers for germplasm characterization and utilization.This information was effective in differentiating or clustering the sweet potato genotypes.A total of 64 alleles were generated using the 20 primers throughout the 20 germplasm samples,with locus IBS97 having the highest number of alleles(5),whereas locus IbU33 had the fewest alleles(2).The alleles varied in size from 105(IbU31)to 213 base pairs(IBS34).The Polymorphism Information Content(PIC)values for the loci IbL46 and IBS97 varied from 0.445 to 0.730.IBS97 has the highest number of effective alleles(3.704),compared to an average of 2.520.The average Shannon’s diversity index(H)was 1.003,ranging from 0.673 in IbU3 to 1.432 in IBS97.The value of gene flow(Nm)varied between 0.000 and 0.005,with an average of 0.003,whereas genetic differentiation(FST-values)ranged between 0.901 and 1.000.The sweet potato germplasm included in this study had a broad genetic base.SP1 vs.SP9 and SP12 vs.SP18 germplasm pairings had the greatest genetic distance(GD=0.965),while SP1 vs.SP2 germplasm couples had the least genetic diversity(GD=0.093).Twenty genotypes were classified into two groups in the UPGMA dendrogram,with 16 genotypes classified as group“A”and the remaining four genotypes,SP10,SP18,SP19,and SP20,classified as group“B.”According to cluster analysis,the anticipated heterozygosity(gene diversity)of Nei(1973)was 0.591 on average.In summary,SSR markers successfully evaluated the genetic relationships among the sweet potato accessions used and generated a high level of polymorphism.The results of the present study will be useful for the management of germplasm,improvement of the current breeding strategies,and the release of new cultivars as varieties.展开更多
Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resourc...Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resource.In this study,46192 microsatellite loci were discovered in 70174 unigenes from the transcriptomic data.Among all of the simple sequence repeat(SSR)unit categories,di-nucleotide and tri-nucleotide SSRs accounted for 45.26%and 14.49%,respectively.A total of 108 SSRs were tested,of which 21 were neutral and polymorphic.Seven SSRs were selected for genetics analyses of the O.minor populations in the Bohai Sea,the Yellow Sea,and the southwest coast of the Taiwan Strait region.Significant pairwise F_(st) values were detected among the samples.The UPGMA tree based on genetic distances suggested that the sampling locations could be arranged in three clusters.These markers are evidence that the populations in this region may be structured,with samples from Penghu differing remarkably from those in northern China.The present study characterized genetic markers for population assessment,management,and conservation of O.minor.展开更多
The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of f...The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of fungicides and the development of new cultivars by plant breeding, marker assisted selection (MAS) will be an efficient alternative method to introduce desired genes into the cultivated varieties in a short time period. The Simple sequence repeats (SSR) markers seem to be the most popular genetic marker of choice for MAS. In the present study, we identified 14 new SSR markers in <i>RPV1</i> locus that are associated with downy mildew resistance in grapes. The characterization of the identified markers was carried out on the basis of various parameters such as types of repeat motifs, number of repeats, different classes and structure of microsatellites. Additionally, SSR genotyping in 56 different grape accessions was done to determine the susceptibility or resistance of these accessions to DM.展开更多
Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified an...Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified and analyzed the SSRs in 23 mosquito species using Drosophila melanogaster as reference at the whole-genome level. The results show that SSR numbers (33 076-560 175/genome) and genome sizes (574.57-1342.21 Mb) are significantly positively correlated (R~= 0.8992, P < 0.01), but the correlation in individual species varies in these mosquito species. In six types of SSR, mono- to trinucleotide SSRs are dominant with cumulative percentages of 95.14%-99.00% and densities of 195.65/Mb-787.51/Mb, whereas tetra- to hexanucleotide SSRs are rare with 1.12%-4.22% and 3.76/Mb-40.23/Mb. The (A/T)n,(AC/GT)n and (AGC/GCT)n are the most frequent motifs in mononucleotide, dinucleotide and trinucleotide SSRs, respectively, and the motif frequencies of tetra- to hexanucleotide SSRs appear to be species-specific. The 10-20 bp length of SSRs are dominant with the number of 11() 561 ± 93 482 and the frequency of 87.25%± 5.73% on average, and the number and frequency decline with the increase oflength. Most SSRs(83.34%± 7.72%) are located in intergenic regions, followed by intron regions (11.59%± 5.59%), exon regions (3.74%± 1.95%), and untranslated regions (1.32%± 1.39%). The mono-, di- and trinucleotide SSRs are the main SSRs in both gene regions (98.55%± 0.85%) and exon regions (99.27%± 0.52%). An average of 42.52% of total genes contains SSRs, and the preference for SSR occurrenee in different gene subcategories are species-specific. The study provides useful insights into the SSR diversity, characteristics and distribution in 23 mosquito species of genomes.展开更多
Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificia...Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China.展开更多
The resource of Fenneropenaeus chinensis has declined sharply due to excessive fishing intensity,ecological changes and diseases.In order to supplement the fishing yield and restore resources of F.chinensis,the releva...The resource of Fenneropenaeus chinensis has declined sharply due to excessive fishing intensity,ecological changes and diseases.In order to supplement the fishing yield and restore resources of F.chinensis,the relevant authorities have carried out the activities of stock enhancement and releasing.It can increase biomass and recover resources.However,compared with increasing biomass,there were still few reports on its effect on the recovery of resources.Resource recovery is a process related to whether the released individuals can form a reproductive population.Up to now,there has been a lack of evidence whether the released F.chinensis can complete the entire life history,and form reproduction population.In this study,gravid female shrimp after spawning migration were captured from coastal waters of Haiyang,Qingdao,and Yellow Sea.After identifying parentage relationships using simple sequence repeat(SSR)and mtDNA haplotype,it was finally confirmed that there were eight released individuals in the recapture samples.It was confirmed for the first time that at least part of the released F.chinensis can complete overwintering and reproductive migration,and maintain the migration habits as their wild counterparts.Therefore,we infered that the released shrimp can reproduce under natural conditions,these F.chinensis can form reproductive populations theoretically if without human intervention.These results indicated that enhancenment and release activities have a positive effect on resource recovery.展开更多
The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causin...The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.展开更多
Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with ...Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with 140 individuals derived from the cross of Weihua8(a cultivar)and 12L49(a line with high oleic acid concentration)was used to construct a genetic map and conduct QTL mapping analysis.A total of 103 polymorphic SSR primers were utilized for genotyping the RILs and finally generating the SSR loci.Within the 103 SSR loci,a genetic linkage map,covering a total length of 3592.35 cM of the whole peanut genome,was constructed.Based on the genetic map,sixteen QTLs located on nine linkage groups related to peanut fatty acids were finally identified.Among them,four QTLs were detected associated with various traits simultaneously,which showed genetic stability in relation to fatty acids of peanut.Except for the QTLs for oleic acid,linoleic acid,and linolenic acid,three novel QTLs for arachidic acid and behenic acid were also detected.These QTLs might be helpful for further fine mapping analysis and marker-assisted selection of fatty acids in peanut.展开更多
Assessment of genetic diversity is an essential component in germplasm characterization and conservation.There are three wild rice species in Hainan Province,including Oryza rufipogon Griff.In order to detect the gene...Assessment of genetic diversity is an essential component in germplasm characterization and conservation.There are three wild rice species in Hainan Province,including Oryza rufipogon Griff.In order to detect the genetic diversity of different populations of Oryza rufipogon in Hainan,ISSR(inter-simple sequence repeat)and SSR(simple sequence repeat)markers were used to investigate 180 accessions from six localities in Hainan.Fourteen ISSR primers amplified 185 alleles with 171(92.43%)polymorphic,the number of alleles ranged from 8 to 17,with an average of 13.14 alleles per locus.Thirty-eight pairs of SSR primers used in this study amplified 213 alleles with 190(89.20%)polymorphic,the number of alleles ranged from 2 to 14,with an average of 5.66 alleles per locus.Both ISSR and SSR analyses revealed a high level of genetic diversity in the wild populations.The population with the highest genetic diversity is Wanning(WN),and the population with lowest genetic diversity is Wenchang(WC).The results of a UPGMA cluster using the NTSYS program showed that each population has a low degree of genetic differentiation.Furthermore,the Mantel test revealed that the genetic similarities detected by ISSR and SSR were significantly correlated(r=0.8634,t=93.67)when detecting genetic diversity at the species level.The two molecular marker systems were able to determine the genetic diversity among Oryza rufipogon,and the two groups of indexes obtained by using the two markers have a high level of consistency.展开更多
Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropicaland sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no...Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropicaland sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no major resistant gene waslocated in rice until date. In the present study, a new major quantitative trait locus (QTL) conferring resistance to BLS wasidentified from a highly resistant variety Dular by the employment of Dular/Balilla (DB) and Dular/IR24 (DI) segregationpopulations and was designated qBLSR-11-1. This QTL was located between the simple sequence repeat (SSR) markersRM120 and RM441 on chromosome 11 and could account for 18.1-21.7% and 36.3% of the variance in DB and DIpopulations, respectively. The genetic pattern of rice resistance to BLS was discussed.展开更多
Cigar line Beinhart 1000-1 has effective durable resistance to black shank(BS) and is considered one of the most resistant sources in tobacco(Nicotiana tabacum L.). To investigate the inheritance and identification of...Cigar line Beinhart 1000-1 has effective durable resistance to black shank(BS) and is considered one of the most resistant sources in tobacco(Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci(QTL) for BS response, F2,BC1 F2 individuals and BC1 F2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci(M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC1 F2 population in the field and in BC1 F2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding.展开更多
An F2 population derived from the cross of WB01, an introgression line resistant to brown planthopper (BPH) originated from Oryza rufipogon Griff. and a susceptible indica variety 9311, was developed for genetic analy...An F2 population derived from the cross of WB01, an introgression line resistant to brown planthopper (BPH) originated from Oryza rufipogon Griff. and a susceptible indica variety 9311, was developed for genetic analysis and gene mapping. The population with 303 F2:3 families was genotyped by 141 simple sequence repeat (SSR) markers and used for gene mapping. Two softwares, Mapmaker/Exp 3.0 and Windows QTL Cartographer V2.0 were applied to detect QTLs. Totally, two QTLs resistant to BPH, named temporarily as bph22(t) and bph23(t), were identified to locate on chromosomes 4 and 8, individually had LOD values of 2.92 and 3.15, and explained 11.3% and 14 .9% of the phenotypic variation, respectively.展开更多
Because there are thousands of peach cultivars,cultivar classification is a critical step before starting a breeding project.Various molecular markers such as simple sequence repeats(SSRs)can be used.In this study,67 ...Because there are thousands of peach cultivars,cultivar classification is a critical step before starting a breeding project.Various molecular markers such as simple sequence repeats(SSRs)can be used.In this study,67 polymorphic primers produced 302 bands.Higher values for SI index(1.903)suggested higher genetic variability in the genotype under investigation.Mean values for observed alleles(Na),expected heterozygosity(He),effective alleles(Ne),Nei’s information index(h),and polymorphic information content(PIC)were 4.5,0.83,5.45,0.83,and 0.81,respectively.The dendrogram constructed based on Jaccard’s similarity coefficients outlined four distinct clusters in the entire germplasm.In addition,an analysis of molecular variance(AMOVA)showed that70.68%of the total variation was due to within-population variation,while 29.32%was due to variation among populations.According to this research,all primers were successfully used for the peach accessions.The EST-SSR markers should be useful in peach breeding programs and other research.展开更多
This study was conducted to determine the parent-off spring genetic structure of the pedunculate oak(Quercus robur L.),sessile oak(Q.petraea[Matt.]Liebl.)and their hybrids.Forty half-sib Quercus families and their mat...This study was conducted to determine the parent-off spring genetic structure of the pedunculate oak(Quercus robur L.),sessile oak(Q.petraea[Matt.]Liebl.)and their hybrids.Forty half-sib Quercus families and their maternal trees originating from one tree stand in southern Lithuania were analyzed using SSR and RAPD markers.Based on a preliminary study of leaf morphological traits,the individuals separated into six groups.The studied halfsib oak families were also compared for allelic diversity,including group variations;genotypic structure;genetic diversity;and the degree of genetic subdivision and diff erentiation.The level of genetic variation and subdivision was lower in the hybrid families than in the families of the parental species.Genotypic analysis of the half-sibling off spring showed the asymmetric nature of interspecifi c hybridization processes of pedunculate and sessile oaks in mixed stands.展开更多
Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mam...Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.展开更多
Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to ...Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island,China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010.Four more populations were later found on Hainan and in Vietnam.In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species,we identified infraspecific molecular markers in the present study,using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively.The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp,and exhibited a typical angiosperm quadripartite structure.Six plastid hotspot regions with the Pi> 0.01(trnH-psbA,psbA-trnK,rpl22,ndhE,ndhG-ndhI rps15-ycf1),and 1621 polymorphic gSSRs,as well as 1657 candidate SNPs in 237 variant nuclear genes were identified,thereby providing important information for further genetic studies.展开更多
Pineapple plant was always injured due to low temperature. Breeding varieties with high cold tolerance was the supreme way to resolve this problem and identifying cold tolerance of germplasms collected was necessary. ...Pineapple plant was always injured due to low temperature. Breeding varieties with high cold tolerance was the supreme way to resolve this problem and identifying cold tolerance of germplasms collected was necessary. In this study, SSR locus around homologous sequences of cold-tolerant genes w</span><span style="font-family:"">as</span><span style="font-family:""> searched and screened using MD-2 (cold-tolerant variety) and Tainong 17 (cold-sensitive variety). Seventy three pairs of primers of which PCR results were different between these two varieties were gotten. PCRs were performed using these as primers and genomic DNA of germplasms collected as templates. Six pairs of primers were found that their PCR results were in good consistent with cold tolerance. Using GLM (General linear model) association <span>mapping analysis, two SSR markers linked to cold tolerance were found. Their</span> efficiency was verified further using pineapple germplasms with high cold tolerance which had been validated in field by cold wave. They will be used in cold-tolerant breeding of pineapple in the future.展开更多
To clarify the most appropriate sample size for obtaining phenotypic data for a single line,we investigated the main-effect QTL(M-QTL) of a quantitative trait plant height(ph) in a recombinant inbred line(RIL) populat...To clarify the most appropriate sample size for obtaining phenotypic data for a single line,we investigated the main-effect QTL(M-QTL) of a quantitative trait plant height(ph) in a recombinant inbred line(RIL) population of rice(derived from the cross between Xieqingzao B and Zhonghui 9308) using five individual plants in 2006 and 2009.Twenty-six ph phenotypic datasets from the completely random combinations of 2,3,4,and 5 plants in a single line,and five ph phenotypic datasets from five individual plants were used to detect the QTLs.Fifteen M-QTLs were detected by 1 to 31 datasets.Of these,qph7a was detected repeatedly by all the 31 ph datasets in 2006 and explained 11.67% to 23.93% of phenotypic variation;qph3 was detected repeatedly by all the 31 datasets and explained 5.21% to 7.93% and 11.51% to 24.46% of phenotypic variance in 2006 and 2009,respectively.The results indicate that the M-QTL for a quantitative trait could be detected repeatedly by the phenotypic values from 5 individual plants and 26 sets of completely random combinations of phenotypic data within a single line in an RIL population under different environments.The sample size for a single line of the RIL population did not affect the efficiency for identification of stably expressed M-QTLs.展开更多
Betula utilis D.Don.is an important species of alpine Himalaya and forms the major treeline component of western Himalaya.The different populations of B.utilis are declining and are under high risk.In the present stud...Betula utilis D.Don.is an important species of alpine Himalaya and forms the major treeline component of western Himalaya.The different populations of B.utilis are declining and are under high risk.In the present study,novel expressed sequence tag-simple sequence repeat(EST-SSR)primers were developed from expressed sequence tag(EST)data of different Betula species.Of the10,796 designed primers,the percentages of di-,tri-,tetra-,penta-,and hexa-repeats were 36%,35%,15%,5.5%and7.7%,respectively.For validation,50 primers were synthesized randomly and were characterized in 20 different B.utilis accessions from north-western Himalaya.Of these,45 primers amplified fragments in a range of 1-6.The 24 polymorphic primers produced 111 fragments in aggregate with 4.6 fragments on average.Polymorphism information content(PIC)ranged from 0.288 in marker BUMS-24 to 0.497 in BUMS-3 and BUMS-7,with an average of 0.447 among polymorphic markers.Dendrogram based on Jaccard’s similarity coefficient and UPGMA method showed that newly developed SSR markers distinguished twenty accessions of B.utilis into two groups.As no SSR markers were available in this species,the newly developed markers will foster molecular genetics research and conservation efforts for this species.展开更多
基金The work was financially supported by National Agricultural Technology Program-II Project(NATP-2)BARC Component Bangladesh Agricultural Research Council,Farmgate,Dhaka-1215+2 种基金Bangladesh Agricultural Research Institute(BARI),Joydebpur,Gazipur 1701The work was partially supported by the Taif University Researchers Supporting Project No.(TURSP-2020/39)Taif University,Taif,Saudi Arabia.
文摘Every breeding program that aims to create new and improved cultivars with desired traits mostly relies on information related to genetic diversity.Therefore,molecular characterization of germplasms is important to obtain target cultivars with desirable traits.Sweet potato[Ipomoea batatas(L.)Lam]is widely considered the world’s most important crop,with great diversity in morphological and phenotypic traits.The genetic diversity of 20 sweet potato germplasms originating from Bangladesh,CIP,Philippines,Taiwan,and Malaysia were compared,which was accomplished by genetic diversity analysis by exploring 20 microsatellite DNA markers for germplasm characterization and utilization.This information was effective in differentiating or clustering the sweet potato genotypes.A total of 64 alleles were generated using the 20 primers throughout the 20 germplasm samples,with locus IBS97 having the highest number of alleles(5),whereas locus IbU33 had the fewest alleles(2).The alleles varied in size from 105(IbU31)to 213 base pairs(IBS34).The Polymorphism Information Content(PIC)values for the loci IbL46 and IBS97 varied from 0.445 to 0.730.IBS97 has the highest number of effective alleles(3.704),compared to an average of 2.520.The average Shannon’s diversity index(H)was 1.003,ranging from 0.673 in IbU3 to 1.432 in IBS97.The value of gene flow(Nm)varied between 0.000 and 0.005,with an average of 0.003,whereas genetic differentiation(FST-values)ranged between 0.901 and 1.000.The sweet potato germplasm included in this study had a broad genetic base.SP1 vs.SP9 and SP12 vs.SP18 germplasm pairings had the greatest genetic distance(GD=0.965),while SP1 vs.SP2 germplasm couples had the least genetic diversity(GD=0.093).Twenty genotypes were classified into two groups in the UPGMA dendrogram,with 16 genotypes classified as group“A”and the remaining four genotypes,SP10,SP18,SP19,and SP20,classified as group“B.”According to cluster analysis,the anticipated heterozygosity(gene diversity)of Nei(1973)was 0.591 on average.In summary,SSR markers successfully evaluated the genetic relationships among the sweet potato accessions used and generated a high level of polymorphism.The results of the present study will be useful for the management of germplasm,improvement of the current breeding strategies,and the release of new cultivars as varieties.
基金supported by the National Natural Science Foundation of China(No.31672257)the National Key Research and Development Program of China(No.2020YFD0900705).
文摘Octopus minor(Sasaki 1920)is an important commercial cephalopod species in China.This species has declined sharply in recent years.Hence,genetic studies of O.minor are imperative to exploit and manage the wild resource.In this study,46192 microsatellite loci were discovered in 70174 unigenes from the transcriptomic data.Among all of the simple sequence repeat(SSR)unit categories,di-nucleotide and tri-nucleotide SSRs accounted for 45.26%and 14.49%,respectively.A total of 108 SSRs were tested,of which 21 were neutral and polymorphic.Seven SSRs were selected for genetics analyses of the O.minor populations in the Bohai Sea,the Yellow Sea,and the southwest coast of the Taiwan Strait region.Significant pairwise F_(st) values were detected among the samples.The UPGMA tree based on genetic distances suggested that the sampling locations could be arranged in three clusters.These markers are evidence that the populations in this region may be structured,with samples from Penghu differing remarkably from those in northern China.The present study characterized genetic markers for population assessment,management,and conservation of O.minor.
文摘The cultivation of grapes is severely impacted by the emergence of downy mildew (DM) disease which negatively affects quality and yield possibly resulting in heavy losses. Due to certain shortcomings in the usage of fungicides and the development of new cultivars by plant breeding, marker assisted selection (MAS) will be an efficient alternative method to introduce desired genes into the cultivated varieties in a short time period. The Simple sequence repeats (SSR) markers seem to be the most popular genetic marker of choice for MAS. In the present study, we identified 14 new SSR markers in <i>RPV1</i> locus that are associated with downy mildew resistance in grapes. The characterization of the identified markers was carried out on the basis of various parameters such as types of repeat motifs, number of repeats, different classes and structure of microsatellites. Additionally, SSR genotyping in 56 different grape accessions was done to determine the susceptibility or resistance of these accessions to DM.
基金the National Natural Science Foundation of China(31672363,31372265)the Par-Eu Scholars Program(20136666)+2 种基金the Coordinated Research Project of the International Atomic En?ergy Agency(18268)the National Key Program of Science and Tech no logy Foundation Work of China(2015FY210300)and the Science and Technology Research Project of Chongqing Municipal Education Commission(KJ 1600304).
文摘Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified and analyzed the SSRs in 23 mosquito species using Drosophila melanogaster as reference at the whole-genome level. The results show that SSR numbers (33 076-560 175/genome) and genome sizes (574.57-1342.21 Mb) are significantly positively correlated (R~= 0.8992, P < 0.01), but the correlation in individual species varies in these mosquito species. In six types of SSR, mono- to trinucleotide SSRs are dominant with cumulative percentages of 95.14%-99.00% and densities of 195.65/Mb-787.51/Mb, whereas tetra- to hexanucleotide SSRs are rare with 1.12%-4.22% and 3.76/Mb-40.23/Mb. The (A/T)n,(AC/GT)n and (AGC/GCT)n are the most frequent motifs in mononucleotide, dinucleotide and trinucleotide SSRs, respectively, and the motif frequencies of tetra- to hexanucleotide SSRs appear to be species-specific. The 10-20 bp length of SSRs are dominant with the number of 11() 561 ± 93 482 and the frequency of 87.25%± 5.73% on average, and the number and frequency decline with the increase oflength. Most SSRs(83.34%± 7.72%) are located in intergenic regions, followed by intron regions (11.59%± 5.59%), exon regions (3.74%± 1.95%), and untranslated regions (1.32%± 1.39%). The mono-, di- and trinucleotide SSRs are the main SSRs in both gene regions (98.55%± 0.85%) and exon regions (99.27%± 0.52%). An average of 42.52% of total genes contains SSRs, and the preference for SSR occurrenee in different gene subcategories are species-specific. The study provides useful insights into the SSR diversity, characteristics and distribution in 23 mosquito species of genomes.
基金Supported by the National Key R&D Program of China (No. 2019YFD0901202)the Key-Area Research and Development Program of Guangdong Province (No. 2021B0202020002)+1 种基金the China Postdoctoral Science Foundation (No. 2021M693677)the Yellow Fin Bream Seed System Building Project (2021)
文摘Yellowfin seabream Acanthopagrus latus is an important economic fish in Chinese coastal areas.Given its narrow distribution and overfishing,the genetic diversity of yellowfin seabream has been restricted for artificial breeding and reproduction.We performed full-length transcriptome sequencing and assembly of the genome of yellowfin seabream.A total of 68086 unigenes were obtained,with an N50 of 3391 bp on average length of 2933 bp.A total number of 50593 expressed sequence tags linked to simple sequence repeats(EST-SSR)were identified,among them dinucleotide repeats(40.6%)and AC/GT motifs(38.5%)were the most frequent.Of the 190 EST-SSRs for which PCR primer pairs were designed,150 primer pairs successfully amplified target loci and 15 SSRs showed high polymorphism.The alleles per locus ranged 6-50 on average of 25.3.The expected and observed heterozygosity varied from 0.632 to 0.969 and from 0.519 to 0.953,respectively.The polymorphic index content(PIC)values of each locus ranged 0.587-0.966 on average of 0.851.Among six yellowfin seabream population samples preliminarily tested for genetic diversity and differentiation,the Fangchenggang(FCG)population in Guangxi Province had the highest mean observed heterozygosity(H_(o))value(0.786),whereas the Zhangzhou(ZZ)population in Fujian Province had the lowest(0.678).The pairwise fixation index(Fst)values indicated significant population differentiation among six yellowfin seabream populations.This study provided evidence for the usefulness of the transcriptomic resource information and EST-SSR markers for natural resource conservation,population genetics,and breeding studies of yellowfin seabream in South China.
基金Laoshan Laboratory under contract No.LSKJ202203803。
文摘The resource of Fenneropenaeus chinensis has declined sharply due to excessive fishing intensity,ecological changes and diseases.In order to supplement the fishing yield and restore resources of F.chinensis,the relevant authorities have carried out the activities of stock enhancement and releasing.It can increase biomass and recover resources.However,compared with increasing biomass,there were still few reports on its effect on the recovery of resources.Resource recovery is a process related to whether the released individuals can form a reproductive population.Up to now,there has been a lack of evidence whether the released F.chinensis can complete the entire life history,and form reproduction population.In this study,gravid female shrimp after spawning migration were captured from coastal waters of Haiyang,Qingdao,and Yellow Sea.After identifying parentage relationships using simple sequence repeat(SSR)and mtDNA haplotype,it was finally confirmed that there were eight released individuals in the recapture samples.It was confirmed for the first time that at least part of the released F.chinensis can complete overwintering and reproductive migration,and maintain the migration habits as their wild counterparts.Therefore,we infered that the released shrimp can reproduce under natural conditions,these F.chinensis can form reproductive populations theoretically if without human intervention.These results indicated that enhancenment and release activities have a positive effect on resource recovery.
基金Supported by the International Science Partnership Program of the Chinese Academy of Sciences(No.133137KYSB20200002)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050304)the Natural Science Foundation of Shandong Province(Nos.ZR2021MC151,ZR2021QD158)。
文摘The sea star Asterias amurensis is widely viewed as a severe“marine pest”because of its broad feeding habits.Over the past few decades,A.amurensis undergoes massive and sporadic population outbreaks worldwide,causing extensive economic and ecological losses to the local aquaculture industry and marine ecosystem.Understanding the genetic diversity and population structure of A.amurensis can provide vital information for resource management.By analyzing the polymorphism of the mitochondrial cytochrome C oxidase subunit I(COI)gene and ten simple sequence repeat(SSR)microsatellites markers,the genetic diversity and population structure of A.amurensis of four populations along the northern coast of China was uncovered.A total of 36 haplotypes were identified,and a main haplotype was found in four populations.The Qingdao(QD)population displayed the highest genetic diversity among all the populations.The AMOVA and pairwise F_(st)showed that there was small but statistically significant population differentiation among the four populations,especially between QD and Weihai(WH).Moreover,the principal component analysis(PCA)and admixture analysis showed that several individuals in Yantai(YT)and Dalian(DL)had little genetic association with other individuals.Overall,this study provided useful information of the genetic diversity and population structure of A.amurensis and will contribute to the resource management of A.amurensis in China.
基金supported by the Development Plan of Science and Technology Project of Jilin Province in China[20220508054RC].
文摘Peanut,with high oil content,has been a major oil and food crop globally.The compositions of the fatty acids are the common factors in determining the oil quality.In the present study,an F2 segregated population with 140 individuals derived from the cross of Weihua8(a cultivar)and 12L49(a line with high oleic acid concentration)was used to construct a genetic map and conduct QTL mapping analysis.A total of 103 polymorphic SSR primers were utilized for genotyping the RILs and finally generating the SSR loci.Within the 103 SSR loci,a genetic linkage map,covering a total length of 3592.35 cM of the whole peanut genome,was constructed.Based on the genetic map,sixteen QTLs located on nine linkage groups related to peanut fatty acids were finally identified.Among them,four QTLs were detected associated with various traits simultaneously,which showed genetic stability in relation to fatty acids of peanut.Except for the QTLs for oleic acid,linoleic acid,and linolenic acid,three novel QTLs for arachidic acid and behenic acid were also detected.These QTLs might be helpful for further fine mapping analysis and marker-assisted selection of fatty acids in peanut.
文摘Assessment of genetic diversity is an essential component in germplasm characterization and conservation.There are three wild rice species in Hainan Province,including Oryza rufipogon Griff.In order to detect the genetic diversity of different populations of Oryza rufipogon in Hainan,ISSR(inter-simple sequence repeat)and SSR(simple sequence repeat)markers were used to investigate 180 accessions from six localities in Hainan.Fourteen ISSR primers amplified 185 alleles with 171(92.43%)polymorphic,the number of alleles ranged from 8 to 17,with an average of 13.14 alleles per locus.Thirty-eight pairs of SSR primers used in this study amplified 213 alleles with 190(89.20%)polymorphic,the number of alleles ranged from 2 to 14,with an average of 5.66 alleles per locus.Both ISSR and SSR analyses revealed a high level of genetic diversity in the wild populations.The population with the highest genetic diversity is Wanning(WN),and the population with lowest genetic diversity is Wenchang(WC).The results of a UPGMA cluster using the NTSYS program showed that each population has a low degree of genetic differentiation.Furthermore,the Mantel test revealed that the genetic similarities detected by ISSR and SSR were significantly correlated(r=0.8634,t=93.67)when detecting genetic diversity at the species level.The two molecular marker systems were able to determine the genetic diversity among Oryza rufipogon,and the two groups of indexes obtained by using the two markers have a high level of consistency.
文摘Bacterial leaf streak (BLS) is one of the important limiting factors to rice production in southern China and other tropicaland sub-tropical areas in Asia. Resistance to BLS was found to be a quantitative trait and no major resistant gene waslocated in rice until date. In the present study, a new major quantitative trait locus (QTL) conferring resistance to BLS wasidentified from a highly resistant variety Dular by the employment of Dular/Balilla (DB) and Dular/IR24 (DI) segregationpopulations and was designated qBLSR-11-1. This QTL was located between the simple sequence repeat (SSR) markersRM120 and RM441 on chromosome 11 and could account for 18.1-21.7% and 36.3% of the variance in DB and DIpopulations, respectively. The genetic pattern of rice resistance to BLS was discussed.
基金supported by grants from the Agricultural Science and Technology Innovation Program (ASTIP-TRIC01)National Natural Science Foundation of China (31571738)
文摘Cigar line Beinhart 1000-1 has effective durable resistance to black shank(BS) and is considered one of the most resistant sources in tobacco(Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci(QTL) for BS response, F2,BC1 F2 individuals and BC1 F2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci(M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC1 F2 population in the field and in BC1 F2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding.
基金funded by the Science and Technology Project for Agriculture in China: Conservation, Utilization and Exploration of Agricultural Wild Plant Sources (2010-2014)
文摘An F2 population derived from the cross of WB01, an introgression line resistant to brown planthopper (BPH) originated from Oryza rufipogon Griff. and a susceptible indica variety 9311, was developed for genetic analysis and gene mapping. The population with 303 F2:3 families was genotyped by 141 simple sequence repeat (SSR) markers and used for gene mapping. Two softwares, Mapmaker/Exp 3.0 and Windows QTL Cartographer V2.0 were applied to detect QTLs. Totally, two QTLs resistant to BPH, named temporarily as bph22(t) and bph23(t), were identified to locate on chromosomes 4 and 8, individually had LOD values of 2.92 and 3.15, and explained 11.3% and 14 .9% of the phenotypic variation, respectively.
基金The work was supported by Payme-Noor University of Tehran,Iran and Shahid Chamran University of Ahvaz(AG1396-Grant_Faculty of Agriculture).
文摘Because there are thousands of peach cultivars,cultivar classification is a critical step before starting a breeding project.Various molecular markers such as simple sequence repeats(SSRs)can be used.In this study,67 polymorphic primers produced 302 bands.Higher values for SI index(1.903)suggested higher genetic variability in the genotype under investigation.Mean values for observed alleles(Na),expected heterozygosity(He),effective alleles(Ne),Nei’s information index(h),and polymorphic information content(PIC)were 4.5,0.83,5.45,0.83,and 0.81,respectively.The dendrogram constructed based on Jaccard’s similarity coefficients outlined four distinct clusters in the entire germplasm.In addition,an analysis of molecular variance(AMOVA)showed that70.68%of the total variation was due to within-population variation,while 29.32%was due to variation among populations.According to this research,all primers were successfully used for the peach accessions.The EST-SSR markers should be useful in peach breeding programs and other research.
基金partly supported by the long-term research programme Sustainable Forestry and Global Changes implemented by the Lithuanian Research Centre for Agriculture and Forestry
文摘This study was conducted to determine the parent-off spring genetic structure of the pedunculate oak(Quercus robur L.),sessile oak(Q.petraea[Matt.]Liebl.)and their hybrids.Forty half-sib Quercus families and their maternal trees originating from one tree stand in southern Lithuania were analyzed using SSR and RAPD markers.Based on a preliminary study of leaf morphological traits,the individuals separated into six groups.The studied halfsib oak families were also compared for allelic diversity,including group variations;genotypic structure;genetic diversity;and the degree of genetic subdivision and diff erentiation.The level of genetic variation and subdivision was lower in the hybrid families than in the families of the parental species.Genotypic analysis of the half-sibling off spring showed the asymmetric nature of interspecifi c hybridization processes of pedunculate and sessile oaks in mixed stands.
基金supported by the National Natural Science Foundation of China(Grant Nos.31900188,31970225)Natural Science Foundation of Zhejiang Province(Grant No.LY19C030007).
文摘Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.
基金the National Natural Science Foundation of China(grant number 31970225 and 31900181)the Zhejiang Provincial Natural Science Foundation(grant number LY19C030007)the Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources(PFGR202104).
文摘Wenchengia alternifolia(Lamiaceae),the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered(CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island,China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010.Four more populations were later found on Hainan and in Vietnam.In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species,we identified infraspecific molecular markers in the present study,using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively.The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp,and exhibited a typical angiosperm quadripartite structure.Six plastid hotspot regions with the Pi> 0.01(trnH-psbA,psbA-trnK,rpl22,ndhE,ndhG-ndhI rps15-ycf1),and 1621 polymorphic gSSRs,as well as 1657 candidate SNPs in 237 variant nuclear genes were identified,thereby providing important information for further genetic studies.
文摘Pineapple plant was always injured due to low temperature. Breeding varieties with high cold tolerance was the supreme way to resolve this problem and identifying cold tolerance of germplasms collected was necessary. In this study, SSR locus around homologous sequences of cold-tolerant genes w</span><span style="font-family:"">as</span><span style="font-family:""> searched and screened using MD-2 (cold-tolerant variety) and Tainong 17 (cold-sensitive variety). Seventy three pairs of primers of which PCR results were different between these two varieties were gotten. PCRs were performed using these as primers and genomic DNA of germplasms collected as templates. Six pairs of primers were found that their PCR results were in good consistent with cold tolerance. Using GLM (General linear model) association <span>mapping analysis, two SSR markers linked to cold tolerance were found. Their</span> efficiency was verified further using pineapple germplasms with high cold tolerance which had been validated in field by cold wave. They will be used in cold-tolerant breeding of pineapple in the future.
基金supported by the grants from the Chinese Natural Science Foundation(Grant No.31071398)the National Program on Super Rice Breeding,the Ministry of Agriculture(Grant No.2010-3)+1 种基金National High Technology Research and Development Program of China(Grant No.2006AA10Z1E8)the Provincial Program of ‘8812’,Zhejiang Province,China(Grant No.8812-1)
文摘To clarify the most appropriate sample size for obtaining phenotypic data for a single line,we investigated the main-effect QTL(M-QTL) of a quantitative trait plant height(ph) in a recombinant inbred line(RIL) population of rice(derived from the cross between Xieqingzao B and Zhonghui 9308) using five individual plants in 2006 and 2009.Twenty-six ph phenotypic datasets from the completely random combinations of 2,3,4,and 5 plants in a single line,and five ph phenotypic datasets from five individual plants were used to detect the QTLs.Fifteen M-QTLs were detected by 1 to 31 datasets.Of these,qph7a was detected repeatedly by all the 31 ph datasets in 2006 and explained 11.67% to 23.93% of phenotypic variation;qph3 was detected repeatedly by all the 31 datasets and explained 5.21% to 7.93% and 11.51% to 24.46% of phenotypic variance in 2006 and 2009,respectively.The results indicate that the M-QTL for a quantitative trait could be detected repeatedly by the phenotypic values from 5 individual plants and 26 sets of completely random combinations of phenotypic data within a single line in an RIL population under different environments.The sample size for a single line of the RIL population did not affect the efficiency for identification of stably expressed M-QTLs.
基金This work was nancially supported by DBT-IPLS scheme[Reference No.BT/PR4548/INF/22/146/2012].
文摘Betula utilis D.Don.is an important species of alpine Himalaya and forms the major treeline component of western Himalaya.The different populations of B.utilis are declining and are under high risk.In the present study,novel expressed sequence tag-simple sequence repeat(EST-SSR)primers were developed from expressed sequence tag(EST)data of different Betula species.Of the10,796 designed primers,the percentages of di-,tri-,tetra-,penta-,and hexa-repeats were 36%,35%,15%,5.5%and7.7%,respectively.For validation,50 primers were synthesized randomly and were characterized in 20 different B.utilis accessions from north-western Himalaya.Of these,45 primers amplified fragments in a range of 1-6.The 24 polymorphic primers produced 111 fragments in aggregate with 4.6 fragments on average.Polymorphism information content(PIC)ranged from 0.288 in marker BUMS-24 to 0.497 in BUMS-3 and BUMS-7,with an average of 0.447 among polymorphic markers.Dendrogram based on Jaccard’s similarity coefficient and UPGMA method showed that newly developed SSR markers distinguished twenty accessions of B.utilis into two groups.As no SSR markers were available in this species,the newly developed markers will foster molecular genetics research and conservation efforts for this species.
