Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Luo, Xier; Zhou, Yuan; Zhang, Bing; Zhang, Yi; Wang, Xiaobo; Tong-qing, Feng; Li, Zhipeng; Cui, Kuiqing; Wang, Zhiqiang; Luo, Chen; Li, Hui; Deng, Yanfei; Lu, Fenghua; Han, Jianlin; Miao, Yongwang; Mao, Huaming; Yi, Xiaoyan; Ai, Cheng; Wu, Shigang; Li, Alun; Wu, Zhichao; Zhuo, Zijun; Giang, Do Da; Mitra, Bikash; Vahidi, Mohammad Farhad; Mansoor, Shahid; Al-Bayatti, Sahar Ahmed; Sari, Eka Puspita; Gorkhali, Neena Amatya; Prastowo, Sigit; Shafique, Laiba; Ye, Guoyou; Qian, Qian; Chen, Baoshan; Shi, Deshun; Ruan, Jue; Liu, Qingyou

doi:10.1093/nsr/nwaa024

Cited by 47 publications

(53 citation statements)

References 77 publications

(63 reference statements)

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“…Most of these (94%) live in Asia (Luo et al . 2020). The swamp‐type buffaloes are used in China and south‐east Asia (35 million) as draft animals.…”

Section: The Bovine Speciesmentioning

confidence: 99%

“…(j) Domestic river‐type buffaloes are found in India, Sri Lanka, Pakistan, south Iraq, several Balkan countries, Italy, Egypt and Brazil (Mason & Cockrill 1974; Luo et al . 2020). (k) The range of domestic swamp‐type water buffaloes includes the Yangtze river basin in China, south China, Indochina, Nepal, Indonesia, the Philippines and Brazil, whereas small wild populations of the wild water buffaloes are found in India, Sri Lanka, Bhutan, Nepal, Myanmar and Thailand (Hedges et al .…”

Section: The Bovine Speciesmentioning

confidence: 99%

“…The river buffalo (2 n = 50) and swamp buffalo (2 n = 48) have different karyotypes (Fischer & Ulbrich 1967), but are interfertile and have formed hybrid populations in south China and Bangladesh (Luo et al . 2020; Zhang et al . 2016).…”

Section: Phylogeny and Evolutionmentioning

confidence: 99%

“…Selection targeting the dairy production of the river buffalo and the draught power of the swamp buffalo is likely to have led to divergent domestication traits (Luo et al . 2020). There are only few data on the similarities between domestic and wild buffaloes (Zhang et al .…”

Section: Phylogeny and Evolutionmentioning

confidence: 99%

“…2020a; Luo et al . 2020) and there may have been domestic introgression into the wild populations and vice versa.…”

Section: Phylogeny and Evolutionmentioning

confidence: 99%

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Evolution and domestication of the Bovini species

et al. 2020

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Summary Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species – taurine cattle, zebu and yak – and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y‐chromosomal DNA. The high diversity of European breeds has been shaped through isolation‐by‐distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

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“…Most of these (94%) live in Asia (Luo et al . 2020). The swamp‐type buffaloes are used in China and south‐east Asia (35 million) as draft animals.…”

Section: The Bovine Speciesmentioning

confidence: 99%

Section: The Bovine Speciesmentioning

confidence: 99%

Section: Phylogeny and Evolutionmentioning

confidence: 99%

Section: Phylogeny and Evolutionmentioning

confidence: 99%

“…2020a; Luo et al . 2020) and there may have been domestic introgression into the wild populations and vice versa.…”

Section: Phylogeny and Evolutionmentioning

confidence: 99%

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Evolution and domestication of the Bovini species

et al. 2020

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Recovering High‐Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation

2022

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Metagenomic datasets of host‐associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two‐step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low‐depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low‐ and high‐depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.

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