Microsatellite selection candidate associated with reproduction trait in Indonesian Friesian Holstein using published studies

Vanessa, Rebecca; Prastowo, Sigit; Nugroho, T; Widyas, N; Susilowati, Ari; Sutarno, .

doi:10.1063/1.5054459

Cited by 4 publications

(5 citation statements)

References 25 publications

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“…The combination of the INRA032 locus with other microsatellite loci will improve the quality of information on the genetic diversity of local buffalo, thereby increasing the accuracy of decision-making regarding conservation measures. In addition, based on previous studies, it was also explained that the INRA032 locus is associated with reproductive characteristics (calving traits) and body conformation (hocks, rear leg set, rear view) in dairy cattle (Harder et al 2006;Buitenhuis et al 2007;Vanessa et al 2018). Therefore, future research needs to investigate the relationship between the INRA032 locus and other microsatellite markers to morphological characters associated with superior traits in local buffaloes in Indonesia.…”

Section: Resultsmentioning

confidence: 99%

“…One of the microsatellite markers that has been widely used in the assessment of genetic diversity in buffalo populations is the INRA032 locus which is located on chromosome 11 (Vaiman et al, 1994). Not only in buffalo, the use of the INRA032 locus in microsatellite-based genetic diversity assessments has also been applied to dairy cattle and horses (Vanessa et al, 2018;Sukri et al, 2022). Several previous researches have used the INRA032 locus in microsatellite-based genetic diversity assessment of buffaloes in Indonesia, specifically in Kudus (Central Java), East Java, and West Nusa Tenggara populations (Sukri, 2014;Amin & Lestari, 2014;Lathifah, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus

Rahmawati¹,

Basith²,

Lestari³

2023

JRBA

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This study focused on the application of microsatellite markers at the INRA032 locus for genetic diversity assessment in buffalo (Bubalus bubalis) populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total number of samples used was 16, each population represented by 8 samples. Genetic diversity assessment parameters include allele frequency, the Polymorphism Information Content (PIC) and heterozygosity. The results showed that based on the INRA032 locus, the Tuban buffalo population had a higher allele frequency range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC value in both populations was 0.39, so it can be concluded that the INRA032 locus is informative enough to detect polymorphisms in both populations. The percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher than the Tuban population at 50%, suggesting that the genetic diversity of the two populations is still quite high despite the decreasing trend in population numbers.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus

Rahmawati¹,

Basith²,

Lestari³

2023

JRBA

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“…We screened in triplicate 14 microsatellite loci (CSSM22, CSSM16, CSSM19, BM1818, Cer14, ILSTS06, CSSM66, Haut14, CSPS115, INRA35, ETH225, CSRM60, BM888, BM4208) reported to be polymorphic in European red deer (Kuehn et al, 2003; Zhou et al, 2015). We selected these markers based on their reported polymorphisms, chromosome locations and amplicon sizes in multiple studies on red deer (Bishop et al, 1994; Moore et al, 1994; DeWoody et al, 1995; Thieven et al, 1995; Kühn et al, 1996; Vanessa et al, 2014).…”

Section: Methodsmentioning

confidence: 99%

Genetic insights to assist management of the Critically Endangered hangul Cervus hanglu hanglu in the Kashmir Himalaya

Narayan,

Srivastava,

Sreedharan

et al. 2023

Oryx

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The hangul Cervus hanglu hanglu, a Critically Endangered mountain ungulate of Jammu and Kashmir, India, faces the imminent threat of population loss and extinction. Effective management of its largest viable population in Dachigam National Park in the Kashmir Himalaya requires reliable demographic information. Using 14 microsatellite markers we identified 293 individuals (208 females and 85 males) through faecal analysis, and generated data on the genetic status and population size of the hangul in its winter habitat. The mean expected and observed heterozygosities of 0.62 and 0.59 are comparable to those of several red deer Cervus elaphus populations elsewhere. The effective population sizes were 46.3 and 93.7 when the frequencies of rare alleles were considered to be 0.050 and 0.010, respectively. The average mean kinship of the population was 0.34, and there was no evidence of a recent bottleneck event. In genetic mark–recapture analysis the best model included an effect of sex on both detection and recapture probabilities. Detection of males was highest in November, coinciding with the hangul breeding season, whereas detection of females was highest in December. Our estimate of the hangul population using genetic mark–recapture with bootstrapping was 394 individuals. To our knowledge, this is the first study to use genetic data to estimate the population of the hangul. It will guide future studies of this subspecies and also serve as an impetus for identifying founder animals for captive breeding, and for connecting the population in Dachigam National Park with the other small, isolated populations to ensure the long-term survival of this subspecies.

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“…Of these, HEL5 exhibited significant heterozygosity deficit and consequent deviation from HWE in 12 out of 14 studied populations. Both the loci have been reported to be associated with production and/or reproduction traits in cattle [29][30][31]. Specifically, the homozygous long alleles at HEL5 (allele size 159-169) were significantly associated (p = 0.022) with long calving interval in Brangus-Ibage cattle, a composite breed with taurine and zebu ancestry [29].…”

Section: Basic Diversity Measures and Hardy-weinberg Equilibriummentioning

confidence: 98%

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

et al. 2021

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The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

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Microsatellite selection candidate associated with reproduction trait in Indonesian Friesian Holstein using published studies

Cited by 4 publications

References 25 publications

Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus

Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus

Genetic insights to assist management of the Critically Endangered hangul Cervus hanglu hanglu in the Kashmir Himalaya

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

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