Exploring the Structure of Haplotype Blocks and Genetic Diversity in Chinese Indigenous Pig Populations for Conservation Purpose

Abstract

Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.05 were obtained for further analysis. In general, there are similar within-breed genetic diversities (He, Ho, Pn, Ar) among these 7 pig populations in the Taihu Lake region. Average values for the inbreeding coefficients estimates in the 7 populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen a continuous decline in Ne estimates over time with FJ and SW populations having a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection pressure than other Chinese pig breeds. The average genetic distances among the 7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269 (EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the number of haplotype blocks and haplotype diversity was also presented. This study provide a deep understanding of the current situation of conservation in this region, thereby uncovering the pertinent insight to better formulate more reasonable preservation policies for the government departments and breeding planners to follow-up.

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

“…Then, F ROH based on different ROH length categories was calculated, respectively. Compared with Taihu pigs, the F ROH 1 – 5 Mb values of DSE pigs were almost consistent with the inbreeding coefficients of small Meishan pigs and Shawutou pigs ( Zhao et al, 2019 ). And F ROH > 5 Mb was lower than F ROH < 5 Mb in each DSE pig subgroup.…”

“…Ar provides complementary information to gene diversity. The results presented in this study reflected that DSE pigs had less Ar compared with Taihu pigs (Zhao et al, 2019). In general, DSE pigs expressed the lower genetic diversity than that of some other Chinese indigenous pigs, which prompted us to be conscious of the importance of accelerating scientific conservation of DSE pigs.…”

“…Exploring the genetic characterization of DSE pigs could help for preserving genomic variability, advancing scientific conservation, and contributing to sustainability ( Weitzman, 1993 ). Population genetic data, such as single-nucleotide polymorphism (SNP), are often used to demonstrate population structure and genetic diversity in some other Chinese indigenous pigs, such as Jiangxi native pigs, Henan native pigs, Taihu native pigs, and so on ( Wang et al, 2018 ; Qiao et al, 2019 ; Zhao et al, 2019 ). But limited genetic information–associated literatures were reported about DSE pigs, which reflected that people know little about genetic characteristics of DSE pigs.…”

Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

“…Most academic effort in the field of genetic diversity management over the past few decades has primarily been focused on optimal management for small populations of conservation concern where mating in the entire population can be controlled (Ballou & Lacy, 1995;Fernández, Toro, & Caballero, 2001, 2004Kettunen, Daverdin, Helfjord, & Berg, 2017;López-Cortegano et al, 2019;Sonesson & Meuwissen, 2001). Similarly, in livestock, conservation of genomic diversity in combination with genomic selection can occur at the level of entire herds or regional populations, though also suffers from geographic partitioning and localization of conservation efforts (Bosse et al, 2015;Bruford et al, 2015;Herrero-Medrano et al, 2014;Ramljak et al, 2018;Zhao et al, 2019). In contrast, dog breeds, as well as breeds in other companion species such as cats and horses, have populations which are typically maintained by networks of individual breeders.…”

Optimal Management of Genetic Diversity in Subdivided Populations

“…Here we have addressed the question of which marker diversity parameters should be better considered for making conservation management decisions in a subdivided population. For multiallelic markers (such as microsatellite loci) or biallelic ones (such as SNPs) that can be analyzed as multiallelic ones if considering multi-SNP haplotypes ( e.g., Zhao et al, 2019), decisions can be taken on expected heterozygosity or allelic diversity measures. We have investigated the outcome of a subdivided population maintained with different optimization procedures aimed at maximizing heterozygosity or allelic diversity.…”