Evolutionary origin of genomic structural variations in domestic yaks

Xinfeng Liu; Wenyu Liu; Johannes A. Lenstra; Zeyu Zheng; Xiaoyun Wu; Jiao Yang; Bowen Li; Yongzhi Yang; Qiang Qiu; Hongyu Liu; Kexin Li; Chunnian Liang; Xian Guo; Xiaoming Ma; Richard J. Abbott; Minghui Kang; Ping Yan; Jianquan Liu

doi:10.1038/s41467-023-41220-x

Evolutionary origin of genomic structural variations in domestic yaks

Xinfeng Liu, Wenyu Liu, Johannes A. Lenstra, Zeyu Zheng, Xiaoyun Wu, Jiao Yang, Bowen Li, Yongzhi Yang, Qiang Qiu, Hongyu Liu, Kexin Li, Chunnian Liang, Xian Guo, Xiaoming Ma, Richard J. Abbott, Minghui Kang, Ping Yan^*, Jianquan Liu^*

^*Corresponding author for this work

School of Biology

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Abstract

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.

Original language	English
Article number	5617
Number of pages	14
Journal	Nature Communications
Volume	14
DOIs	https://doi.org/10.1038/s41467-023-41220-x
Publication status	Published - 19 Sept 2023

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@article{0ba3786bf0834e128c387fe6a1724be0,

title = "Evolutionary origin of genomic structural variations in domestic yaks",

abstract = "Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.",

author = "Xinfeng Liu and Wenyu Liu and Lenstra, {Johannes A.} and Zeyu Zheng and Xiaoyun Wu and Jiao Yang and Bowen Li and Yongzhi Yang and Qiang Qiu and Hongyu Liu and Kexin Li and Chunnian Liang and Xian Guo and Xiaoming Ma and Abbott, {Richard J.} and Minghui Kang and Ping Yan and Jianquan Liu",

note = "This work was supported by the Second Tibetan Plateau Scientific Expedition and Research program (Grant no. 2019QZKK0502 to J.Q.L.), Agricultural Science and Technology Innovation Program (Grant no. 25-LZIHPS-01 to P.Y.), National Natural Science Foundation of China (Grant no. U22A20447 to B.W.L.), National Key Research and Development Programs (Grant no. 2021YFD1200901 to K.X.L.), National Youth Talent Support Program (to Q.Q.) and Lanzhou University University{\textquoteright}s “Double First-Class” Guided Project Team Building-Funding-Research Startup Fee and International Collaboration 111 Programme (Grant no. BP0719040). All the computation works were supported by the Big Data Computing Platform for Western Ecological Environment and Regional Development, and the Supercomputing Center of Lanzhou University.",

year = "2023",

month = sep,

day = "19",

doi = "10.1038/s41467-023-41220-x",

language = "English",

volume = "14",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature publishing group",

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T1 - Evolutionary origin of genomic structural variations in domestic yaks

AU - Liu, Xinfeng

AU - Liu, Wenyu

AU - Lenstra, Johannes A.

AU - Zheng, Zeyu

AU - Wu, Xiaoyun

AU - Yang, Jiao

AU - Li, Bowen

AU - Yang, Yongzhi

AU - Qiu, Qiang

AU - Liu, Hongyu

AU - Li, Kexin

AU - Liang, Chunnian

AU - Guo, Xian

AU - Ma, Xiaoming

AU - Abbott, Richard J.

AU - Kang, Minghui

AU - Yan, Ping

AU - Liu, Jianquan

N1 - This work was supported by the Second Tibetan Plateau Scientific Expedition and Research program (Grant no. 2019QZKK0502 to J.Q.L.), Agricultural Science and Technology Innovation Program (Grant no. 25-LZIHPS-01 to P.Y.), National Natural Science Foundation of China (Grant no. U22A20447 to B.W.L.), National Key Research and Development Programs (Grant no. 2021YFD1200901 to K.X.L.), National Youth Talent Support Program (to Q.Q.) and Lanzhou University University’s “Double First-Class” Guided Project Team Building-Funding-Research Startup Fee and International Collaboration 111 Programme (Grant no. BP0719040). All the computation works were supported by the Big Data Computing Platform for Western Ecological Environment and Regional Development, and the Supercomputing Center of Lanzhou University.

PY - 2023/9/19

Y1 - 2023/9/19

N2 - Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.

AB - Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.

U2 - 10.1038/s41467-023-41220-x

DO - 10.1038/s41467-023-41220-x

M3 - Article

SN - 2041-1723

VL - 14

JO - Nature Communications

JF - Nature Communications

M1 - 5617

ER -

Evolutionary origin of genomic structural variations in domestic yaks

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