Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated wholegenome sequencing data fro...Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated wholegenome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient(Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia(SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex(C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.展开更多
During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying thi...During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.展开更多
Aurochs(Bos primigenius),once widely distributed in Afro-Eurasia,became extinct in the early 1600 s.However,their phylogeography and relative contributions to domestic cattle remain unknown.In this study,we analyzed 1...Aurochs(Bos primigenius),once widely distributed in Afro-Eurasia,became extinct in the early 1600 s.However,their phylogeography and relative contributions to domestic cattle remain unknown.In this study,we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison(Bison priscus)excavated in East Asia,dating from 43,000 to 3,590 years ago.These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis.Ourfindings revealed significant genetic divergence between East Asian aurochs and their European,Near Eastern,and African counterparts on the basis of both mitochondrial and nuclear genomic data.Furthermore,we identified evidence of geneflow from East Asian aurochs into ancient and present-day taurine cattle,suggesting their potential role in facilitating the environmental adaptation of domestic cattle.展开更多
基金supported by the National Natural Science Foundation of China(32050410304,32002140,31822052,91431572381)National Thousand Youth Talents Plan to Y.J。
文摘Understanding how evolutionary pressures related to climate change have shaped the current genetic background of domestic animals is a fundamental pursuit of biology. Here, we generated wholegenome sequencing data from native goat populations in Iraq and Pakistan. Combined with previously published data on modern, ancient(Late Neolithic to Medieval periods), and wild Capra species worldwide, we explored the genetic population structure, ancestry components, and signatures of natural positive selection in native goat populations in Southwest Asia(SWA). Results revealed that the genetic structure of SWA goats was deeply influenced by gene flow from the eastern Mediterranean during the Chalcolithic period, which may reflect adaptation to gradual warming and aridity in the region. Furthermore, comparative genomic analysis revealed adaptive introgression of the KITLG locus from the Nubian ibex(C. nubiana) into African and SWA goats. The frequency of the selected allele at this locus was significantly higher among goat populations located near northeastern Africa. These results provide new insights into the genetic composition and history of goat populations in the SWA region.
基金supported by the National Key R&D Program of China(2021YFD1200400 and 2021YFF1001000)the National Natural Science Foundation of China(32102523,32372854,31861143014,32260823,and 32172706)+5 种基金the Key Research and Development Program of Xizang Autonomous Region of China(XZ202301ZY0008N)the Yunnan Expert Workstations(202305AF150156),the China Agriculture Research System of MOF and MARA(CARS-37)the Postdoctoral Fellowship Program of CPSF(GZC20232149)the Program of Yunling Scholar and Yunling Cattle Special Program of Yunnan Joint Laboratory of Seeds and Seeding Industry(202205AR070001)the Construction of Yunling Cattle Technology Innovation Center and Industrialization of Achievements(2019ZG007)Finally,we thank the High-Performance Computing(HPC)Center of Northwest A&F University(NWAFU)and Hefei Advanced Computing Center for providing computing resources.
文摘During the past 3000 years,cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia,ultraviolet(UV)radiation,and extreme cold.The genetic mechanism underlying this rapid adaptation is not yet well understood.Here,we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations,including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m.Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries.We found that recently selected genes in Tibetan cattle were related to body size(HMGA2 and NCAPG)and energy expenditure(DUOXA2).We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes,covering 0.64%–3.26%of their genomes,which included introgressed genes responsible for hypoxia response(EGLN1),cold adaptation(LRP11),DNA damage repair(LATS1),and UV radiation resistance(GNPAT).We observed that introgressed yak alleles were associated with noncoding variants,including those in present EGLN1.In Tibetan cattle,three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1,suggesting that these genomic variants enhance hypoxia tolerance.Taken together,our results indicated complex adaptation processes in Tibetan cattle,where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.
基金supported by the National Natural Science Foundation of China(41820104008,U2202207,U23A20161,T2222030 and 32102523)the earmarked fund for the China Agriculture Research System of MOF and MARA(CARS-37)+1 种基金the Chinese Universities Scientific Fund(2452021153)the Independent Research Fund Denmark(8028-00005B).
文摘Aurochs(Bos primigenius),once widely distributed in Afro-Eurasia,became extinct in the early 1600 s.However,their phylogeography and relative contributions to domestic cattle remain unknown.In this study,we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison(Bison priscus)excavated in East Asia,dating from 43,000 to 3,590 years ago.These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis.Ourfindings revealed significant genetic divergence between East Asian aurochs and their European,Near Eastern,and African counterparts on the basis of both mitochondrial and nuclear genomic data.Furthermore,we identified evidence of geneflow from East Asian aurochs into ancient and present-day taurine cattle,suggesting their potential role in facilitating the environmental adaptation of domestic cattle.
