Data_Sheet_1_Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis.xlsx

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.

伊犁巴尔奇羊的产羔生产力是一项综合的母性性状，被视为羊肉生产中最重要的经济性状。本研究的目的是应用替代的全基因组关联研究（GWAS）方法，随后进行基因集富集分析（GSEA），对伊犁巴尔奇羊的基因组进行探究，以识别影响妊娠结果及分娩后羔羊生长的基因。本研究考虑了出生和断奶时的三个母性综合性状。这些性状包括后代出生体重、出生时胎群平均体重、出生时胎群总重量、后代断奶体重、断奶时胎群平均体重以及断奶时胎群总重量。对原始表型以及估计的育种值进行了GWAS分析。与出生时综合性状相关的显著单核苷酸多态性（SNPs）位于RDX、FDX1、ARHGAP20、ZC3H12C、THBS1和EPG5等基因内部或附近。所识别的基因和通路与妊娠相关，例如胎盘中的自噬、胎盘产生孕酮、胎盘形成、钙离子转运以及母体免疫反应。对于断奶时的综合性状，确定了影响采食量和食物保存、乳腺细胞骨架结构发育以及脂肪酸、蛋白质和B-12等乳制品生产的基因（NR2C1、VEZT、HSD17B4、RSU1、CUBN、VIM、PRLR和FTH1）和通路。结果表明，与母性起源的其他效应相比，妊娠期间的钙离子转运以及分娩后通过母乳喂养羔羊可以对体重增长产生最大的影响。