Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class <scp>II</scp><i><scp>BoLA‐DRB3</scp></i> allele

Takeshima, Shin‐nosuke; Miyasaka, T.; Matsumoto, Yuki; Gao, Xue; Díaz, Víctor; Rogberg-Muñoz, A.; Giovambattista, Guillermo; Ortiz, Marta; Oltra, J.; Kanemaki, Masato T.; Onuma, Misao; Aida, Yoko

doi:10.1111/tan.12481

Cited by 25 publications

(39 citation statements)

References 29 publications

(52 reference statements)

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“…As shown in Table 3, the values obtained in Myanmar cattle were similar to those estimated for other cattle breeds Gene diversity, HWE, and neutrality testing of BoLA-DRB3 variants found in Myanmar cattle populations As mentioned above, n a ranged from 33 in the Holstein-Friesian crossbreed to 58 in the Pyer Sein native breed, while h e and h o were both higher than 0.86 in all three populations ( Table 2). These indexes are evidence of high diversity values for Myanmar cattle populations, which is similar to the results reported for other bovine breeds which have been evaluated by PCR-SBT, and characteristic of MHC class II DR genes [18,22,23,26,29]. When we evaluated the populations using the HWE test, two of the three Myanmar populations were in equilibrium, while native breed Shwe Ni signi cantly deviated from its theoretical values (Table 2), probably because of the signi cant proportions of homozygous animals found in this study (F IS = 0.1197, p < 0.0001).…”

Section: The Average D N and D S Substitutions Insupporting

confidence: 85%

“…The π values within Pyer Sein, Shwe Ni and Holstein-Friesian crossbreed were 0.090, 0.080 and 0.080, respectively, while the mean number of pairwise differences was 20.96, 17.89 and 20.09, respectively. These nucleotide diversity values all fall within the upper end of the range reported (π range = 0.068-0.083; NPD range = 16.31-20.04) for other bovine breeds when using PCR-SBT genotyping methods [18,22,23,26,29].…”

Section: Nucleotide and Amino Acid Diversity In The Bola-drb3 Allelessupporting

confidence: 65%

“…As a result of these studies there are 144 described BoLA-DRB3 alleles for bovines, and 303 subtypes listed in the Immuno Polymorphism Database (IPD-MHC) [30,31]. In addition, previous studies [16][17][18][19][20][21][22][23][24][25][26][27] have shown an even distribution of BoLA-DRB3 polymorphisms between the major bovine types (Bos taurus and B. indicus) and breeds. This is likely as a result of various factors including breed origin, arti cial or natural selection and geographical distribution.…”

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Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Giovambattista

Moe

Polat

et al. 2020

Preprint

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Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

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Section: The Average D N and D S Substitutions Insupporting

confidence: 85%

Section: Nucleotide and Amino Acid Diversity In The Bola-drb3 Allelessupporting

confidence: 65%

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confidence: 99%

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Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Giovambattista

Moe

Polat

et al. 2020

Preprint

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“…Blood samples from 855 cattle, comprising four farms from Argentina ( N = 424), two from Bolivia ( N = 159), five from Paraguay ( N = 139), and two from Peru ( N = 133), were obtained [Figure S1 (Supporting information), Table ]. In addition, previously reported data from Japanese Holsteins ( N = 102), Japanese Jerseys ( N = 69), Chilean Holstein ( N = 113), and Yacumeño Creoles ( N = 113) were included in the present study . This experiment is approved by the Committee on the Ethics of Animals for Research at the National University of LA PLATA (Certificate date 26 May 2014) and by the Committee on the Ethics of Animals for Research at Universidad Austral de Chile (Certificate No.…”

Section: Methodsmentioning

confidence: 99%

Characterization of bovine MHC class II DRB3 diversity in South American Holstein cattle populations

et al. 2015

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Holstein cattle dominate the global milk production industry because of their outstanding milk production, however, this breed is susceptible to tropical endemic pathogens and suffers from heat stress and thus fewer Holstein populations are raised in tropical areas. The bovine major histocompatibility complex (BoLA)-DRB3 class II gene is used as a marker for disease and immunological traits, and its polymorphism has been studied extensively in Holstein cattle from temperate and cold regions. We studied the genetic diversity of the BoLA-DRB3 gene in South American Holstein populations to determine whether tropical populations have diverged from those bred in temperate and cold regions by selection and/or crossbreeding with local native breeds. We specifically studied Exon 2 of this gene from 855 South American Holstein individuals by a polymerase chain reaction (PCR) sequence-based typing method. We found a high degree of gene diversity at the allelic (Na > 20 and He > 0.87) and molecular (π > 0.080) levels, but a low degree of population structure (FST = 0.009215). A principal components analysis and tree showed that the Bolivian subtropical population had the largest genetic divergence compared with Holsteins bred in temperate or cold regions, and that this population was closely related to Bolivian Creole cattle. Our results suggest that Holstein genetic divergence can be explained by selection and/or gene introgression from local germplasms. This is the first examination of BoLA-DRB3 in Holsteins adapted to tropical environments, and contributes to an ongoing effort to catalog bovine MHC allele frequencies by breed and location.

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“…Polymorphism of exon 2 of the BoLA-DRB3 gene was studied in over 30 breeds of cattle. On the basis of the revealed alelle frequencies, there were determined the parameters of population-genetic structure of South African (Haikukutu et al, 2017), Mongolian, Yakut and Kalmyk (Ruzina et al, 2010), Argentinian Creole (Giovambattista et al, 2001), Chilean (Takeshima et al, 2015b), Indian (Das et al, 2012), Japanese (Takeshima et al, 2003;Miyasaka et al, 2012), Philippine native (Takeshima et al, 2014) and South American populations of cattle (Takeshima et al, 2015a).…”

Section: Introductionmentioning

confidence: 99%

Population genetic structure of the Ukrainian black-pied dairy breed with the genome BoLA-DRB3

Suprovych

Dyman

Suprovych

et al. 2018

Regul. Mech. Biosyst.

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The second exon of the BoLA-DRB3 gene has the highest level of polymorphism among all studied loci of the major histocompatibility complex (MHC) in cattle, which allows it to be used for studying population-genetic structure and assessing the level of biodiversity of populations or comparing the biodiversity of particular herds. According to the results of typing the blood samples of 293 cows using the method of PCR-RLFP, we determined allele frequencies of the BoLA-DRB3 gene for the Ukrainian black-pied dairy breed. The study was conducted on three herds in Khmelnytskyi Oblast: LLC “Kozatska Dolyna 2006” (herd A, n = 122), agrofirm “Perlyna Podillya” (herd B, n = 82) and branch “Ridnyy kray” (herd C, n = 89). In total, 37 alleles were found: herd A 31, herd B 25 and herd C 28. In total, in the three subpopulations seven alleles were found with frequency of over 5%, the total share of which equaled 55.8%. The most widely distributed allele was BoLA-DRB3.2*24, which composed 22.2% of the allele pool of the breed. We determined a high level of observed (0.89 to 0.95) and expected (0.93 to 0.94) heterozygosity. In herds A and B, there was determined domination of homozygotes. Deviation from HWE, calculated using the value of Wright`s individual fixation index, equaled FIS(A) = 0.016 (χ2 = 0.03; P > 0.05) and FIS(B) = 0.044 (χ2 = 0.076; P > 0.05). In herd C, we found excess of heterozygotes FIS(C) = -0.017 (χ2 = 0.026; P > 0.05). Rather low values were determined for the subpopulation fixation index: FST(A) = 0.009 (χ2 = 65.9; P < 0.01), FST(B) = 0.012 (χ2 = 47.2; P < 0.05) and FST(C) = 0.003 (χ2 = 14.4; P > 0.05), which were significantly different from the mean value for cattle (FST = 0.078), indicating insignificant reduction of heterozygosity and divergence between the subpopulations by the BoLA-DRB3 gene. To assess genetic diversity, we calculated parameters of effective allele number (Ae) and Shannon’s information index (I). In spite of the different numbers of alleles found in the selections, it was suggested that for assessing their diversity, an efficiency index will be used which shows the share of effective alleles among all alleles found in a subpopulation (Ae/Nа). The calculated values of the parameters equaled: herd A Ae = 14.9, Ae/Nа = 0.48, I = 3.05; herd B Ae = 14.5, Ae/Nа = 0.58, I = 2.87; herd C Ae = 16.4, Ae/Nа = 0.59, I = 3.01. Frequencies of BoLA-DRB3 alleles were used for calculating genetic similarity and standard genetic distances according to Nei. Cows of herds B and C were found to be more genetically affinitive by the BoLA-DRB3 gene. Standard genetic distance between them was the lowest D = 0.13, which coincides with the geographic locations and historical development of these populations. The results of the study prove that the studied herds have a high level of polymorphism. Frequency characteristics, values of expected heterozygosity, effective allele number, efficiency index and Shannon’s information index compared to the similar parameters for Holstein, black-pied and some other local breeds of cattle indicate the high genetic diversity of the studied subpopulations of the Ukrainian black-pied dairy breed.

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Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class IIBoLA‐DRB3 allele

Cited by 25 publications

References 29 publications

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Characterization of bovine MHC class II DRB3 diversity in South American Holstein cattle populations

Population genetic structure of the Ukrainian black-pied dairy breed with the genome BoLA-DRB3

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