title: Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus).
abstract: Dairy goats are one of the most utilized domesticated animals in China. Here, we selected extreme populations based on differential fecundity in two Laoshan dairy goat populations. Utilizing deep sequencing we have generated 68.7 and 57.8 giga base of sequencing data, and identified 12,458,711 and 12,423,128 SNPs in the low fecundity and high fecundity groups, respectively. Following selective sweep analyses, a number of loci and candidate genes in the two populations were scanned independently. The reproduction related genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 and THEM4 were specifically selected in the high fecundity group whereas KDM6A, TENM1, SWI5 and CYM were specifically selected in the low fecundity group. A sub-set of genes including SYCP2, SOX5 and POU3F4 were localized both in the high and low fecundity selection windows, suggesting that these particular genes experienced strong selection with lower genetic diversity. From the genome data, the rare nonsense mutations may not contribute to fecundity, whereas nonsynonymous SNPs likely play a predominant role. The nonsynonymous exonic SNPs in SETDB2 and CDH26 which were co-localized in the selected region may take part in fecundity traits. These observations bring us a new insights into the genetic variation influencing fecundity traits within dairy goats.
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Fang-Nong
authors.initials: FN
authors.lastname: Lai
authors.affiliation: Shandong International Biotechnology Park, Yantai 264670, China.
authors.forename: Hong-Li
authors.initials: HL
authors.lastname: Zhai
authors.affiliation: Qingdao Research Institute of Husbandry and Veterinary, Qingdao 266300, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Jun-Yu
authors.initials: JY
authors.lastname: Ma
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Shun-Feng
authors.initials: SF
authors.lastname: Cheng
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ge
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Jun-Jie
authors.initials: JJ
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Rui-Qian
authors.initials: RQ
authors.lastname: Zhang
authors.affiliation: College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Ling-Jiang
authors.initials: LJ
authors.lastname: Min
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Jiu-Zhou
authors.initials: JZ
authors.lastname: Song
authors.affiliation: Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Shen
mesh_terms: D000818:Animals; D005260:Female; D005298:Fertility / Q000235:genetics; D016678:Genome; D055106:Genome-Wide Association Study; D006041:Goats / Q000235:genetics*; D008098:Litter Size / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D000073336:Whole Genome Sequencing