Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs).

Heli Xiong,Chaochao Peng,Dongmei Xi,Weidong Deng,Xiaoming He,Xingneng Liu,Jing Li

doi:10.5194/aab-63-193-2020

Abstract

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population , which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

Highlights

IntroductionLanping black-boned sheep (LPBB) was first discovered in the 1950s and characterized by black pigmentation on skin and internal organs compared to the reddish coloration in Lanping normal sheep (LPN) (Deng et al, 2008; Li et al, 2018); the pigmentation pattern is similar to that in silky fowl of China (Li et al, 2018; Deng et al, 2006)
The level of polymorphic SNP (Pn) present in Lanping black-boned sheep (LPBB) population was 0.8390, which was slightly lower than Lanping normal sheep (LPN) population but greatly lower than the other six populations; this reflected that LPBB population had lower loci displaying polymorphism compared to the remaining populations (Table 1)
We estimated for the first time the genetic diversity and genetic origin of Lanping black-boned sheep by using genome-wide SNP data

Summary

Introduction

Lanping black-boned sheep (LPBB) was first discovered in the 1950s and characterized by black pigmentation on skin and internal organs compared to the reddish coloration in Lanping normal sheep (LPN) (Deng et al, 2008; Li et al, 2018); the pigmentation pattern is similar to that in silky fowl of China (Li et al, 2018; Deng et al, 2006) Attributable to their tender and tasty meat quality and no special smell of mutton, LPBB stands out among Lanping local sheep breeds and has been designated as a novel genetic resource by the Chinese Ministry of Agriculture (Li et al, 2018).

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