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.
Highlights
The goat (Capra hircus) is one of the oldest domesticated animal species[1]
Inactive homozygous mutations occurring in transforming growth factor β(TGFB) superfamily members including BMP15 or GDF9 results in decreased ovulation rates leading to eventual sterility[6,7]
A previous study demonstrated that a non-synonymous single nucleotide polymorphisms (SNPs) G1534A mutation in exon 2 of bone morphogenetic protein 4 (BMP4) within the India goat breeds Black-Bengal and Jakhrana are related to variations seen in prolificacy[8]
Summary
The goat (Capra hircus) is one of the oldest domesticated animal species[1]. From the statistical data available from the UN Food and Agricultural Organization in 2011, there are more than 1000 breeds of goats and 924 million live goats around the world[2]. Litter size appears to be controlled by multiple genes and factors[5] including, ovarian follicular development, oocyte maturation, ovulation, fertilization, embryogenesis, embryo implantation, and uterine receptivity. These fecundity traits are regulated by gonadotropins, ovarian steroid hormones, and growth factors including luteinzing hormone (LH), follicle stimulating hormone (FSH), 17β-estradiol (E2), progesterone (Prog), and activin A Two homozygous SNPs (g.151435C >T, g.173057T >C) located in exon 2 and the 3′untranslated region (3′UTR) of the prolactin receptor (PRLR) gene are significantly associated with fecundity in both Guanzhong and Boer goat breeds[9]. It is still critical to select excellent individuals based on the genetic features of interest
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