The objective of this work was to draw up an inventory of environmental and anthropogenic factors linked to indigenous breeding practices of guinea fowl (Numida meleagris) influenced by plumage characteristics. The in...The objective of this work was to draw up an inventory of environmental and anthropogenic factors linked to indigenous breeding practices of guinea fowl (Numida meleagris) influenced by plumage characteristics. The information was collected using the snowball technique and using a formal questionnaire developed (AU-IBAR, 2015). The dominant plumage is pearl gray with a frequency of 38.89% followed by black (13.85%). In total, 154 adult animals were lost by operators with a frequency of 22.95%. According to plumage, white comes first with a frequency of 51.61% followed by Lavender plumage (36.58%). Predation is the major constraint with a frequency of 35.72%. The guinea fowl most targeted by predators are the white guinea fowl with a frequency of 56.25%, while predation is low for black plumage (25%), royal purple (33.34) and pearl gray (34.69). The pearl gray guinea fowl and the royal purple guinea fowl appear to have a more developed wild instinct, which explains the frequency of recorded escapes. White plumage is perceived as being more docile during breeding and tends to exhibit better resistance to heat stress compared to other phenotypes, making it more valued for traditional rituals. Dark plumage seems more sought after in breeding for its supposed prolificacy, its resistance to infections and its weight. According to breeders, the dominance relationship mainly depends on the number of individuals of the same plumage. Dark plumage in significant numbers in most flocks seems to have dominance in terms of food and choice of sexual partners, which would explain their large numbers.展开更多
Soybean cyst nematode(SCN)is a highly destructive pathogen.The soybean host genome harbors at least two major genes for resistance(rhg1 and Rhg4),as well as a minor locus(SCN3-11).In the present study,a splicing site ...Soybean cyst nematode(SCN)is a highly destructive pathogen.The soybean host genome harbors at least two major genes for resistance(rhg1 and Rhg4),as well as a minor locus(SCN3-11).In the present study,a splicing site in GmSNAP11,the potential causal gene of SCN3-11,was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions.The sequence information was used to design a codominant CAPS marker,GmSNAP11-2565,which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance.Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect(nonsynonymous)locus,GmSNAP11-2307,previously identified in GmSNAP11,revealed linkage disequilibrium(P<0.0001)between the two loci,suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11.GmSNAP11-2565 was accordingly used,along with established markers for GmSNAP18(rhg1)and GmSHMT(Rhg4),to characterize the panel accessions.The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance(20.3%)was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18(12.4%),while the index for accessions carrying alleles for resistance at all of GmSNAP11,GmSNAP18,and GmSHMT was very low(1.9%).Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.展开更多
Soybean cyst nematode(SCN,Heterodera glycines Ichinohe)is one of the most economically destructive pathogens.The soybean line Zhongpin03-5373(ZP),which combines resistance genes from several donors,is highly resistant...Soybean cyst nematode(SCN,Heterodera glycines Ichinohe)is one of the most economically destructive pathogens.The soybean line Zhongpin03-5373(ZP),which combines resistance genes from several donors,is highly resistant to SCN race 3(SCN3).In our previous study,two QTL(rhg1 and GmSNAP11)were identified in a population of recombinant inbred lines derived from a cross between ZP and the susceptible parent Zhonghuang 13.The two QTL explained around one-third of the resistance,suggesting the presence of further QTL contributing to SCN resistance.In the present study,we used an improved version of the geneticmap comprising the previously applied 1062 molecular markers and 47 newly developed InDel(insertion-deletion)markers.The improved map revealed a novel locus contributing to SCN3 resistance:qSCN3-1,flanked by InDelmarker InDel1-7 and SNPmarker Map-0047,explained 4.55%of the phenotypic variance for resistance to SCN3 and was not involved in digenic epistatic interaction with rhg1 and GmSNAP11.Haplotypes of Map-0047_CAPS(a CAPS marker developed for Map-0047)and InDel1-7 were significantly associated with SCN3 resistance in a panel of 209 resistant and susceptible accessions.Using further allele-combination analysis for three functional markers representing three cloned resistance genes(rhg1,Rhg4,andGmSNAP11)and twomarkers flanking qSCN3-1,we found that adding the resistance allele of qSCN3-1 greatly increased soybean resistance to SCN,even in diverse genetic backgrounds.The qSCN3-1 locus will be useful for marker-assisted polygene pyramid breeding and should be targeted for the future identification of candidate genes.展开更多
Cynodon species can be used for multiple purposes and have high economic and ecological significance.However,the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood,partially due to...Cynodon species can be used for multiple purposes and have high economic and ecological significance.However,the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood,partially due to the limited availability of genomic resources.In this study,we report a chromosome-scale genome assembly of a diploid Cynodon species,C.transvaalensis,obtained by combining Illumina and Nanopore sequencing,BioNano,and Hi-C.The assembly contains 282 scaffolds(~423.42 Mb,N50=5.37 Mb),which cover~93.2%of the estimated genome of C.transvaalensis(~454.4Mb).Furthermore,90.48%of the scaffolds(~383.08 Mb)were anchored to nine pseudomolecules,of which the largest was 60.78Mb in length.Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates,typically with dry summers.The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily,in particular,the Cynodonteae tribe,but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.展开更多
The traditional technique for asexual propagation of Siraitia grosvenori in vitro is adopted widely by pressing the vine, which has a high risk of carrying viral diseases and limits the production of promoted cultivar...The traditional technique for asexual propagation of Siraitia grosvenori in vitro is adopted widely by pressing the vine, which has a high risk of carrying viral diseases and limits the production of promoted cultivars. So this paper reported in vitro regeneration of S. grosvenori by testing for shoot induction from various explant sources such as leaf, petiole and stem. Several phytohormone combinations of TDZ, BA and IAA were examined for shoot regeneration and NAA or IBA for rooting. The highest shoot induction rate （100% of regeneration frequency and 15.3 shoots per explant） in leaf was obtained by incubation on MS medium supplemented with 0.5 mg·L^-1 TDZ, 2.0 mg·L^-1 BA and 0.5 mg·L^-1 IAA; unlike shoot regeneration in leaves, the most efficient bud inductions in petiole and stem explants were initiated on MS medium containing 0.2 mg·L^-1 TDZ, 2.0mg·L^-1 BA and 0.5 mg·L^-1 IAA, in addition, adventitious buds in petiole and stem explants needed to be transformed to MS medium for development; optimal root was obtained when shoots were cultured on 1/2MS medum supplemented with 0.5 mg·L^-1 NAA or 0.5 mg·L^-1 IBA.展开更多
35-40-year experience of the study of geographical cultures in Kazakhstan has allowed accumulating of significant scientific information on test of seed progeny of different origins of Pinus sylvestris. Results on gro...35-40-year experience of the study of geographical cultures in Kazakhstan has allowed accumulating of significant scientific information on test of seed progeny of different origins of Pinus sylvestris. Results on growing of climatic types of the pine in provenance trial plantations of Pavlodarskaya, East-Kazakhstan, Kostanayskaya and Akmolinskaya oblasts of the Republic of Kazakhstan are given. Long-term studies have shown that at growing of different origins in determined conditions with the use of identical agricultural techniques, different silvicultural, selection and economic effects are reached. Analysis of all the available material has been conducted on the basis of which new forest seed zoning is designed and the most productive and stable ecotypes are selected as candidates for sort-populations. Arakaragayskiy ecotype is universal for different zones and site conditions of the pine in Kazakhstan. Chebarkulskiy ecotype has good indices on productivity, stability, quality of plantings and on selection effect. Given geographical ecotypes are recommended as candidates for sort-populations.展开更多
Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the...Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.展开更多
Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can s...Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.展开更多
Genome-wide prediction is a promising approach to boost selection gain in hybrid breeding.Our main objective was to evaluate the potential and limits of genome-wide prediction to identify superior hybrid combinations ...Genome-wide prediction is a promising approach to boost selection gain in hybrid breeding.Our main objective was to evaluate the potential and limits of genome-wide prediction to identify superior hybrid combinations adapted to Northwest China.A total of 490 hybrids derived from crosses among 119 inbred lines from the Shaan A and Shaan B heterotic pattern were used for genome-wide prediction of ten agronomic traits.We tested eight different statistical prediction models considering additive(A)effects and in addition evaluated the impact of dominance(D)and epistasis(E)on the prediction ability.Employing five-fold cross validation,we show that the average prediction ability ranged from 0.386 to 0.794 across traits and models.Six parametric methods,i.e.ridge regression,LASSO,Elastic Net,Bayes B,Bayes C and reproducing kernel Hilbert space(RKHS)approach,displayed a very similar prediction ability for each trait and two non-parametric methods(random forest and support vector machine)had a higher prediction performance for the trait rind penetrometer resistance of the third internode above ground(RPR_TIAG).The models of A+D RKHS and A+D+E RKHS were slightly better for predicting traits with a relatively high non-additive variance.Integrating trait-specific markers into the A+D RKHS model improved the prediction ability of grain yield by 3%,from 0.528 to 0.558.Of all 6328 potential hybrids,selection of the top 44 hybrids would lead to a 6%increase in grain yield compared with Zhengdan 958,a commercially successful hybrid variety.In conclusion,our results substantiate the value of genome-wide prediction for hybrid breeding and suggest dozens of promising single crosses for developing high-yielding hybrids for Northwest China.展开更多
Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,w...Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.展开更多
文摘The objective of this work was to draw up an inventory of environmental and anthropogenic factors linked to indigenous breeding practices of guinea fowl (Numida meleagris) influenced by plumage characteristics. The information was collected using the snowball technique and using a formal questionnaire developed (AU-IBAR, 2015). The dominant plumage is pearl gray with a frequency of 38.89% followed by black (13.85%). In total, 154 adult animals were lost by operators with a frequency of 22.95%. According to plumage, white comes first with a frequency of 51.61% followed by Lavender plumage (36.58%). Predation is the major constraint with a frequency of 35.72%. The guinea fowl most targeted by predators are the white guinea fowl with a frequency of 56.25%, while predation is low for black plumage (25%), royal purple (33.34) and pearl gray (34.69). The pearl gray guinea fowl and the royal purple guinea fowl appear to have a more developed wild instinct, which explains the frequency of recorded escapes. White plumage is perceived as being more docile during breeding and tends to exhibit better resistance to heat stress compared to other phenotypes, making it more valued for traditional rituals. Dark plumage seems more sought after in breeding for its supposed prolificacy, its resistance to infections and its weight. According to breeders, the dominance relationship mainly depends on the number of individuals of the same plumage. Dark plumage in significant numbers in most flocks seems to have dominance in terms of food and choice of sexual partners, which would explain their large numbers.
基金National Key R&D Program for Crop Breeding (2016YFD0100602, 2016YFD0100201)the Agricultural Science and Technology Innovation Program (ASTIP) of the Chinese Academy of Agricultural SciencesNational Science and Technology Platform
文摘Soybean cyst nematode(SCN)is a highly destructive pathogen.The soybean host genome harbors at least two major genes for resistance(rhg1 and Rhg4),as well as a minor locus(SCN3-11).In the present study,a splicing site in GmSNAP11,the potential causal gene of SCN3-11,was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions.The sequence information was used to design a codominant CAPS marker,GmSNAP11-2565,which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance.Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect(nonsynonymous)locus,GmSNAP11-2307,previously identified in GmSNAP11,revealed linkage disequilibrium(P<0.0001)between the two loci,suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11.GmSNAP11-2565 was accordingly used,along with established markers for GmSNAP18(rhg1)and GmSHMT(Rhg4),to characterize the panel accessions.The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance(20.3%)was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18(12.4%),while the index for accessions carrying alleles for resistance at all of GmSNAP11,GmSNAP18,and GmSHMT was very low(1.9%).Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.
基金This research was financed by the National Key Research and Development Program of China(2016YFD0100201)the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences.
文摘Soybean cyst nematode(SCN,Heterodera glycines Ichinohe)is one of the most economically destructive pathogens.The soybean line Zhongpin03-5373(ZP),which combines resistance genes from several donors,is highly resistant to SCN race 3(SCN3).In our previous study,two QTL(rhg1 and GmSNAP11)were identified in a population of recombinant inbred lines derived from a cross between ZP and the susceptible parent Zhonghuang 13.The two QTL explained around one-third of the resistance,suggesting the presence of further QTL contributing to SCN resistance.In the present study,we used an improved version of the geneticmap comprising the previously applied 1062 molecular markers and 47 newly developed InDel(insertion-deletion)markers.The improved map revealed a novel locus contributing to SCN3 resistance:qSCN3-1,flanked by InDelmarker InDel1-7 and SNPmarker Map-0047,explained 4.55%of the phenotypic variance for resistance to SCN3 and was not involved in digenic epistatic interaction with rhg1 and GmSNAP11.Haplotypes of Map-0047_CAPS(a CAPS marker developed for Map-0047)and InDel1-7 were significantly associated with SCN3 resistance in a panel of 209 resistant and susceptible accessions.Using further allele-combination analysis for three functional markers representing three cloned resistance genes(rhg1,Rhg4,andGmSNAP11)and twomarkers flanking qSCN3-1,we found that adding the resistance allele of qSCN3-1 greatly increased soybean resistance to SCN,even in diverse genetic backgrounds.The qSCN3-1 locus will be useful for marker-assisted polygene pyramid breeding and should be targeted for the future identification of candidate genes.
基金the National Natural Science Foundation of China(32071887,31472140)the Beijing Municipal Natural Science Foundation(6182025)。
文摘Cynodon species can be used for multiple purposes and have high economic and ecological significance.However,the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood,partially due to the limited availability of genomic resources.In this study,we report a chromosome-scale genome assembly of a diploid Cynodon species,C.transvaalensis,obtained by combining Illumina and Nanopore sequencing,BioNano,and Hi-C.The assembly contains 282 scaffolds(~423.42 Mb,N50=5.37 Mb),which cover~93.2%of the estimated genome of C.transvaalensis(~454.4Mb).Furthermore,90.48%of the scaffolds(~383.08 Mb)were anchored to nine pseudomolecules,of which the largest was 60.78Mb in length.Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates,typically with dry summers.The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily,in particular,the Cynodonteae tribe,but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.
文摘The traditional technique for asexual propagation of Siraitia grosvenori in vitro is adopted widely by pressing the vine, which has a high risk of carrying viral diseases and limits the production of promoted cultivars. So this paper reported in vitro regeneration of S. grosvenori by testing for shoot induction from various explant sources such as leaf, petiole and stem. Several phytohormone combinations of TDZ, BA and IAA were examined for shoot regeneration and NAA or IBA for rooting. The highest shoot induction rate （100% of regeneration frequency and 15.3 shoots per explant） in leaf was obtained by incubation on MS medium supplemented with 0.5 mg·L^-1 TDZ, 2.0 mg·L^-1 BA and 0.5 mg·L^-1 IAA; unlike shoot regeneration in leaves, the most efficient bud inductions in petiole and stem explants were initiated on MS medium containing 0.2 mg·L^-1 TDZ, 2.0mg·L^-1 BA and 0.5 mg·L^-1 IAA, in addition, adventitious buds in petiole and stem explants needed to be transformed to MS medium for development; optimal root was obtained when shoots were cultured on 1/2MS medum supplemented with 0.5 mg·L^-1 NAA or 0.5 mg·L^-1 IBA.
文摘35-40-year experience of the study of geographical cultures in Kazakhstan has allowed accumulating of significant scientific information on test of seed progeny of different origins of Pinus sylvestris. Results on growing of climatic types of the pine in provenance trial plantations of Pavlodarskaya, East-Kazakhstan, Kostanayskaya and Akmolinskaya oblasts of the Republic of Kazakhstan are given. Long-term studies have shown that at growing of different origins in determined conditions with the use of identical agricultural techniques, different silvicultural, selection and economic effects are reached. Analysis of all the available material has been conducted on the basis of which new forest seed zoning is designed and the most productive and stable ecotypes are selected as candidates for sort-populations. Arakaragayskiy ecotype is universal for different zones and site conditions of the pine in Kazakhstan. Chebarkulskiy ecotype has good indices on productivity, stability, quality of plantings and on selection effect. Given geographical ecotypes are recommended as candidates for sort-populations.
基金supported by the National Key R&D Program of China(2021YFD1201601,2016YFD0100201,2020YFE0202300)the National Natural Science Foundation of China(32072091)+2 种基金the Platform of National Crop Germplasm Resources of China(2016-004,2017-004,2018-004,2019-04,2020-05)the Crop Germplasm Resources Protection(2016NWB036-05,2017NWB036-05,2018NWB03605,2019NWB036-05)the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences(CAASZDRW202109)。
文摘Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.
基金supported by the National Natural Science Foundation of China (NSFC-DFG, 31861133016NSFC, 31970564)。
文摘Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.
基金This work was supported by the National Key Research and Development Program of China(2016YFD0101200 and 2018YFD0100200)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,Ministry of Education.
文摘Genome-wide prediction is a promising approach to boost selection gain in hybrid breeding.Our main objective was to evaluate the potential and limits of genome-wide prediction to identify superior hybrid combinations adapted to Northwest China.A total of 490 hybrids derived from crosses among 119 inbred lines from the Shaan A and Shaan B heterotic pattern were used for genome-wide prediction of ten agronomic traits.We tested eight different statistical prediction models considering additive(A)effects and in addition evaluated the impact of dominance(D)and epistasis(E)on the prediction ability.Employing five-fold cross validation,we show that the average prediction ability ranged from 0.386 to 0.794 across traits and models.Six parametric methods,i.e.ridge regression,LASSO,Elastic Net,Bayes B,Bayes C and reproducing kernel Hilbert space(RKHS)approach,displayed a very similar prediction ability for each trait and two non-parametric methods(random forest and support vector machine)had a higher prediction performance for the trait rind penetrometer resistance of the third internode above ground(RPR_TIAG).The models of A+D RKHS and A+D+E RKHS were slightly better for predicting traits with a relatively high non-additive variance.Integrating trait-specific markers into the A+D RKHS model improved the prediction ability of grain yield by 3%,from 0.528 to 0.558.Of all 6328 potential hybrids,selection of the top 44 hybrids would lead to a 6%increase in grain yield compared with Zhengdan 958,a commercially successful hybrid variety.In conclusion,our results substantiate the value of genome-wide prediction for hybrid breeding and suggest dozens of promising single crosses for developing high-yielding hybrids for Northwest China.
基金supported by the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences(CAAS-ZDRW20210)the National Key Research and Development Program of China(nos.2020YFE0202300 and 2021YFD1201600)the Platform of National Crop Germplasm Resources of China(nos.2016-004 and 2017-004)。
文摘Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.
