Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

Abstract

12 Water buffalo holds the tremendous potential of milk and meat that widespread 13 throughout central and southern China. However, characterization of the population 14 genetics of Chinese buffalo is poorly understood. Using Axiom ® buffalo genotyping 15 array, we performed the genetic diversity, linkage disequilibrium (LD) pattern and 16 signature of selection in the 176 Chinese buffaloes from thirteen breeds. A total of 17 35,547 SNPs passed quality control and were used for further analyses. Population 18 genetic analysis revealed a clear separation between the swamp and river types. Ten 19 Chinese indigenous breeds clustered into the swamp group, Murrah and Nili-Ravi 20 breeds were the river group, and the crossbred breed was closer to the river group.21 Genetic diversity analysis showed that the swamp group had a lower average expected 22 heterozygosities compared to the river group. LD decay distance was much shorter in 23 the swamp group compared with the river group with value of approximately 50 2 0.2 24 Kb. Analysis of runs of homozygosity indicated that extensive remote and recent 25 inbreeding activity was respectively found within swamp and river groups. Moreover, 26 a total of 12 genomic regions under selection were detected between river and swamp 27 groups. Further, 12 QTL regions were found associated with buffalo milk production 28 traits. Some candidate genes within these QTLs were predicted to be involved in the 2 29 cell structure and function, suggesting that these genes might play vital roles in the 30 buffalo milk performance. Our data contribute to our understanding of the 31 characterization of population genetics in Chinese buffaloes, which in turn may be 32 utilized in buffalo breeding programs.33 Author Summary 34 Identifying the causal genes or markers associated with important economic traits in 35 livestock is critical to increasing the production level on the species. However, current 36 understanding of the genetic basis for milk production traits in buffalo is limited.37 Here, we confirmed the divergent evolution, distinct population structure, and LD 38 extent among Chinese buffalo breeds. We also identified 12 QTL regions associated 39 with milk production traits in buffaloes using the selective sweeps and haplotype 40 analysis. Further, a total of 7 genes involved in the cell structure and function were 41 predicted within the identified QTLs. These findings suggested that these genes can 42 serve as the candidate genes associated with buffalo milk production, which hold a 43 vital role in the milk trait improvement of dairy buffalo industry. Introduction45 Water buffalo (Bubalus bubalis), primarily raised for milk, meat and draught power, 46 is an essential part of the agricultural economy of many countries around the world. 47 Broadly, buffalo mainly consists of two types: the river (B. bubalis bubalis; n=50) and 48 swamp (B. bubalis carabensis; n=48), which are primarily distinguished based on 49 their distinct morphology and chromosomal karyotypes [1]. In China, the indi...

Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

“…Among the 167 animals included in this study, we noted two different lineages based on admixture analysis. Similar findings were also found by Lu et al [ 49 ] for Chinese indigenous buffalo breeds. We further noted highly variable nucleotide diversity and Tajima’s D across various chromosomes, which also agrees with previous studies of Asian buffalo breeds that used microsatellite [ 56 – 58 ] and mitochondrial markers [ 59 , 60 ].…”

“…Using the final SNP dataset, we performed PCA, which illustrated two clusters and some outliers (Fig 1 and S2 Table). Our results are consistent with those from Lu et al [49], who also classified water buffalos into two primary groups, with some outliers. To validate the results of PCA, we analyzed the population structure of the water buffalo with the Bayesian clustering algorithm implemented in the STUCTURE program.…”

“…However, comparing our findings directly with previous reports is difficult because of differences in the scale of sampling, given that the level of LD decreases with increasing sample size [ 69 ]. Recently, the pattern of LD decay was reported in various cattle and buffalo breeds across the world, including an Iranian water buffalo population at an average of 57 kb decay [ 70 ], Chinese buffalo breeds at 50 kb for the river group and 15 kb for the swamp group [ 49 ], Tunisian cattle at 73.4 kb [ 71 ], Korean cattle breeds from 26 to 32 kb [ 72 ] and Colombian Creole cattle breeds from 70 to 100 kb [ 73 ].…”

“…Uncharacterized LOC112586670/3-beta-hydroxysteroid-Delta(8) is one of the major enzymes that participates early in lactation in dairy cattle. An lncRNA (LOC112586670) fragment is a candidate gene associated with buffalo milk production [49,74,[83][84][85][86]. From functional analysis of liver microarray data from mid-lactating Holstein cows, delta(7)-isomerase pseudogene (Gene ID: S8_2495291, S8_2495296, S8_2495349) is involved in the cholesterol biosynthesis pathway [87,88].…”