Whole genome sequencing identified genomic diversity and candidated genes associated with economic traits in Northeasern Merino in China

Abstract

Introduction: Northeast Merino (NMS) is a breed developed in Northeast China during the 1960s for wool and meat production. It exhibits excellent traits such as high wool yield, superior meat quality, rapid growth rate, robust disease resistance, and adaptability to cold climates. However, no studies have used whole-genome sequencing data to investigate the superior traits of NMS. Methods: In this study, we investigated the population structure, genetic diversity, and selection signals of NMS using whole-genome sequencing data from 20 individuals. Two methods (integrated haplotype score and composite likelihood ratio) were used for selection signal analysis, and the Fixation Index was used to explore the selection signals of NMS and the other two breeds, Mongolian sheep and South African meat Merino. Results: The results showed that NMS had low inbreeding levels, high genomic diversity, and a pedigree of both Merino breeds and Chinese local breeds. A total length of 14.09 Mb genomic region containing 287 genes was detected using the two methods. Further exploration of the functions of these genes revealed that they are mainly concentrated in wool production performance (IRF2BP2, MAP3K7, and WNT3), meat production performance (NDUFA9, SETBP1, ZBTB38, and FTO), cold resistance (DNAJC13, LPGAT1, and PRDM16), and immune response (PRDM2, GALNT8, and HCAR2). The selection signals of NMS and the other two breeds annotated 87 and 23 genes, respectively. These genes were also mainly focused on wool and meat production performance. Conclusion: These results provide a basis for further breeding improvement, comprehensive use of this breed, and a reference for research on other breeds.

Keywords: Northeast Merino; genetic diversity; population structure; selection signatures; whole-genome sequencing.

FIGURE 1

Population structure and relationships of Northeast Merino compared with other breeds. (A) Admixture plot of 12 sheep breeds using ADMIXTURE with K = 2 and K = 5. (B) Principal component analysis of 12 sheep breeds. (C) A Neighbor-joining phylogenetic tree of the 12 sheep breeds (197 animals). Abbreviations: ALT, Altay; TIB, Tibetan; HUS, Hu; STH, Small-tailed Han; MON, Mongolian; NMS, Northeast Merino; RAM, Rambouillet; SAM, South African Meat Merino; AMS, Australian Merino; CMS, Chinese Merino; SUF, Suffolk; DOR, Dorset.

FIGURE 2

Summary statistics for genetic diversity. (A) Box plots of genomic inbreeding coefficient for each breed. (B) Nucleotide diversity of each breed across the genome in windows of 50 kb with steps of 50 kb. (C) The distribution of expected heterozygosity (H _E) and observed heterozygosity (H _O) in each breed. (D) Linkage disequilibrium (LD) decay in the 12 sheep breeds of China, with a line for each breed.

FIGURE 3

Characterization of positive selection in the genome of Northeast Merino. The red line is the 5 percent threshold. (A) Manhattan plots of selection sweep results for iHS in Northeast Merino. (B) Manhattan plots of selection sweep results for CLR in Northeast Merino.