Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions

Qiu, Qiang; Wang, Lizhong; Wang, Kun; Yang, Yongzhi; Ma, Tao; Wang, Zefu; Zhang, Xiao; Ni, Zengqiang; Hou, Fujiang; Long, Ruijun; Abbott, Richard J.; Lenstra, Johannes A.; Liu, Jianquan

doi:10.1038/ncomms10283

Cited by 209 publications

(245 citation statements)

References 55 publications

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“…Although the draft genome sequence of the Yak has been available for four years, and resequencing studies have since been undertaken [6,33,34] , genetic variation in the Yakmost notably structural variation and genetic comparisons with other bovid species-Remains poorly understood. Moreover, the genome sequence of the Dzo has not been reported until now.…”

Section: Discussionmentioning

confidence: 99%

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

Zhong¹,

Ma²,

Chai³

et al. 2018

Kafkas Univ Vet Fak Derg

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Xin J: Whole genome sequencing of the Dzo: Genetic implications for high altitude adaptation, sterility, and milk and meat production. Kafkas Univ Vet Fak Derg, 24 (6): 835-844, 2018. DOI: 10.9775/kvfd.2018 AbstractThe Dzo, a hybrid between the domestic Yak and cattle found on the Qinghai-Tibetan plateau are commercially important owing to increased meat and milk production, as well as their adaptation to extremely high-altitude environments. To better understand the genomic architecture and adaptive capabilities of this unique domesticated hybrid, we performed whole genome resequencing and compared the genomic architecture and variation of the Dzo to its progenitors: the cattle and Yak. In total, 33.17 M single nucleotide variations (SNVs) were detected between the Dzo and cattle reference genomes. Even though the Dzo is known to be sterile, no genetic signatures associated with sterility were found on the Dzo Y chromosome. On the contrary, our results suggest that the autosomal DMC1 locus (Chromosome 5. 110729098. C>CT) plays a role in the sterility of Dzo, which warrants further exploration of its functions. We integrated the whole genome resequencing data of cattle and Yak to obtain candidate genes with a high degree of variation that might be associated with altitudinal adaptation. We found that the EPAS1 gene, which encodes hypoxia-inducible factor 2α, exhibited significant variation (Chromosome 11.28664187 C>T) between Yak and cattle, and may play a key role in the genetic basis of altitudinal adaptation. In addition, in analyzing differences between the Dzo, Yak, and cattle genomes, we uncovered several additional genomic signatures relevant to high altitude adaptation and meat and milk production. These findings underscore the need for further studies to improve ruminant stock for sustainable agriculture on the Qinghai-Tibet plateau.. Keywords: Dzo: Genome sequencing, Dzo, Altitude adaptation, Sterility, Milk and meat production Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Verimine Etkisi ÖzEvcil Yak ile Qinghai-Tibet platosunda bulunan sığırın bir hibriti olan Dzo artmış et ve süt üretimi ile birlikte aynı zamanda oldukça yüksek rakımlı bölgelere adaptasyonu nedeni ile ticari olarak önem arz etmektedir. Bu özgün evcil hibritin genomik yapısını ve uyum kapasitelerini daha iyi anlamak amacıyla tüm genom sekanslaması yapılarak genomik yapısı ve varyasyonlar Dzonun progenitörleri olan sığır ve Yak ile karşılaştırıldı. Dzo ile sığır referans genomları arasında toplam 33.17 M tek nükleotid varyasyonu belirlendi. Dzo steril olarak bilinmesine rağmen Dzo Y kromozomunda sterilite ile ilgili hiç bir genetik işarete rastlanmadı. Aksine, elde edilen bulgular otozomal DMC1 lokusunun (Kromozom 5. 110729098. C>CT) Dzonun sterilitesinde rol oynadığına işaret etmekte ve bu nedenle de daha ileri araştırılmaların yapılması gerekmektedir. Yüksek rakıma adaptasyon ile ilişkili yüksek oranda varyasyona sahip genlerin araştırılması amacıyla sığır ve Yakın tüm genom sekanslama ve...

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Section: Discussionmentioning

confidence: 99%

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

Zhong¹,

Ma²,

Chai³

et al. 2018

Kafkas Univ Vet Fak Derg

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“…Taurine and zebu cattle are well served in the successful 1000 Bull Genomes Project. A high-quality yak genome and resequencing of numerous individuals have already yielded clues on adaptation and domestication at high altitudes [9, 10]. Whole-genome sequences have been announced or are in the pipeline for bison, gayal and banteng, while, befitting the Year of the Wisent, a high-quality wisent genome sequence has been completed (Wang K, Wang L, Lenstra JA, et al, unpublished).…”

Section: Commentarymentioning

confidence: 99%

The Year of the Wisent

Lenstra

Liu

2016

BMC Biol

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Delving into European prehistory, two recent studies analyze ancient DNA from bison species depicted by our ancestors on the walls of their caves. The DNA tells a story of migrations driven by climate change but leaves some mystery clouding the genetic descent and climate preference of the still-extant wisent, otherwise known as the European bison.See research articles: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0317-7 http://www.nature.com/articles/ncomms13158

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“…Next‐generation sequencing (NGS) technologies are faster and cheaper than Sanger sequencing, which is frequently used in plant studies and allows for a deeper genome variant analysis (Deschamps & Campbell, ; Jackson, Iwata, Lee, Schmutz, & Shoemaker, ). So far, genome sequencing and evolutionary genetics have provided information about the origin, evolution (Ellegren, ; Sedivy, Wu, & Hanzawa, ; Velasco, Hough, Aradhya, & Ross‐Ibarra, ; Wu, Terol, et al, ; Yu et al, ), and domestication (Akagi, Hanada, Yaegaki, Gradziel, & Tao, ; Myles et al, ; Qiu et al, ; Velasco et al, ; Wu, Wang, et al, ). The first 237M long genomic map of P. mume was constructed in 2012, and the actual size of the genome of P. mume was estimated to be about 280M.…”

Section: Introductionmentioning

confidence: 99%

Association between blooming time and climatic adaptation in Prunus mume

Shi

Luo

et al. 2019

Ecology and Evolution

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Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X–76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA‐LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.

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Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions

Cited by 209 publications

References 55 publications

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

Dzo Sığırlarında Tüm Genom Sekanslaması: Yüksek Rakıma Adaptasyon, Sterilite İle Süt ve Et Üretimine Etkisi

The Year of the Wisent

Association between blooming time and climatic adaptation in Prunus mume

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