Ganteil Audrey, Rodriguez-Ramilo Silvia T, Ligonesche Bruno, Larzul Catherine
GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.
SAS NUCLEUS, Le Rheu, France.
Front Genet. 2021 Jan 28;11:584556. doi: 10.3389/fgene.2020.584556. eCollection 2020.
Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.
家畜杂交可用于增加遗传多样性。由此产生的变异性增加与杂交动物的杂合性有关。杂交过程中多样性的演变可以通过基因组数据进行评估。本研究的目的是描述三元杂交产生的动物、亲本纯系动物及其杂交后代中纯合子连续片段（ROH）的模式。杂交方案包括首先将皮特兰公猪与大白母猪杂交，之后皮特兰×大白的后代再与杜洛克公猪杂交。第二次杂交的后代称为G0，G0公猪和G0母猪的后代称为G1。所有动物均使用Illumina SNP60猪芯片进行基因分型。经过筛选后，对2336只动物和48579个常染色体单核苷酸多态性（SNP）进行了分析。结果显示，杜洛克、大白和皮特兰基于ROH的平均近亲繁殖系数分别为0.27±0.05、0.23±0.04和0.26±0.04。在皮特兰×大白杂交后代中检测到了ROH，但纯合片段比其亲本更少、更小。在G0杂交后代中也获得了类似结果。然而，在G1杂交后代中，ROH的数量和大小高于G0亲本。在G0和G1动物的1号、4号、7号、9号、13号、14号和15号猪染色体上检测到了类似的ROH热点区域。在G1动物中观察到了长ROH（>16 Mb），这表明这些区域的重组率较低。这三个杂交群体中这些纯合片段的保守性意味着亲本品种之间共享了一些单倍型。对G0动物ROH热点区域的基因注释鉴定出了与生产性状相关的基因，包括胴体组成和繁殖。这些发现增进了我们对如何管理杂交群体遗传多样性的理解。
