Genetic diversities and population structures of four popular Myanmar local cattle breeds

Abstract

Local cattle breeds are popular in Myanmar because they make excellent draught animals, so it is of fundamental importance that their genetic diversities and population structures are elucidated for breeding and conservation purposes. In this study, we characterized the genetic diversities and population structures of four popular Myanmar local cattle breeds and five native cattle populations from neighboring countries (Bangladesh, Laos, Cambodia, and Vietnam) using the GGP Bovine 50K array. The mean observed and expected heterozygosity estimates using pruned datasets ranged from 0.317 and 0.322, respectively, in Cambodia to 0.448 and 0.421, respectively, in Vietnam South. The four Myanmar local breeds exhibited similar levels of genetic diversity. However, AMOVA revealed significant genetic differentiation among the nine populations (p < 0.00001), and Neighbor‐Net analysis showed that Shan Ngwar Pu was distinct from the other Myanmar local breeds. Furthermore, PCA and population structure analyses revealed that the native cattle from neighboring countries genetically influenced the Myanmar local breeds to some extent and that the genetic origins could also be observed in the local breeds. These findings highlight the importance of Myanmar local breeds as genetic resources and provide useful information for the future development of breeding strategies and conservation management plans.

Feeding pineapple waste silage as roughage source improved the nutrient intakes, energy status and growth performances of growing Myanmar local cattle

“…In the experiments of Gowda et al [ 4 ] and Hattakum et al [ 5 ], Holstein dairy cows and steer were used as experimental animals, which are different in the breed of cattle used in our experiment and Maneerat et al [ 9 ]. In contrast, Myanmar local cattle and fattening Thai steers, both are Zebu type ( Bos indicus ) [ 18 , 19 ], were used, respectively. Jardstedt et al [ 20 ] reported that feed intake was influenced by the breed of cattle, whereas Charolais cattle have a higher feed intake than Hereford cattle.…”

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

“…Firstly, genotypes of 344 VDC were merged with genotypes of 277 reference animals using the command "--merge," resulting in a data set of 623 animals with genotypes of 14,786 overlapping SNPs. Then, a quality control process was applied, which removed 4079 SNPs with either call rate ≤95% or minor allele frequency (MAF) ≤5% using command "--geno 0.05" and "--maf 0.05" (Cheruiyot et al, 2018;Lwin et al, 2018). An individual with a sample call rate of <90% was also removed, using the command "--mind 0.1" (Cheruiyot et al, 2018;Lwin et al, 2018).…”

“…Then, a quality control process was applied, which removed 4079 SNPs with either call rate ≤95% or minor allele frequency (MAF) ≤5% using command "--geno 0.05" and "--maf 0.05" (Cheruiyot et al, 2018;Lwin et al, 2018). An individual with a sample call rate of <90% was also removed, using the command "--mind 0.1" (Cheruiyot et al, 2018;Lwin et al, 2018).…”

“…Knowledge of breed purity and the breed composition is also fundamentally important for breed societies, farmers and scientists. For breed societies, this information is needed for breed registries (Hulsegge et al, 2019) and the identification of suitable selection or crossbreeding plans and for conservation (He et al, 2018b;Lwin et al, 2018). For farmers and nutritionists, this information is necessary to modify diets and housing conditions accordingly because different breeds have different nutrient and environmental requirements (NRC, 2001).…”

“…Black and white cows are considered pure HOL, and those with a higher percentage of black or other colours, usually brown or dark yellow, are considered crossbreds. Recently, due to the development of genotyping technology, the availability of reference genome databases, and the development of statistical packages such as "hierfstat" (Goudet & Jombart, 2015), "ADMIXTURE" (Alexander et al, 2015), "STRUCTURE" (Pritchard et al, 2000) and "LEA" (Frichot & François, 2015); it has become possible to determine genetic diversity, breed purity and breed composition of an animal-based on the genome-wide single nucleotide polymorphism (SNP) markers instead of the pedigree (Gobena et al, 2018;He et al, 2018aHe et al, , 2018bHulsegge et al, 2019;Kuehn et al, 2011;Lwin et al, 2018;Sempéré et al, 2015;Visser et al, 2016). These recent developments should prove to be useful for the determination of genetic diversity and merit in Vietnamese dairy herds where pedigree records are generally unavailable.…”