Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Bakoev, Siroj; Getmantseva, Lyubov; Kostyunina, Olga; Bakoev, Nekruz; Prytkov, Yuri; Усатов, А. В.; Tatarinova, Tatiana V.

doi:10.7717/peerj.11595

Cited by 9 publications

(5 citation statements)

References 45 publications

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“…All selection variants directly related to the number and weight of piglets intersect with different QTLs, including for average daily gain and body weight. Some of these genes were previously directly noted in associative studies with sow fertility and are reviewed by Bakoev et al [28].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

Romanets,

Bakoev,

Romanets

et al. 2024

Anim Biosci

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Objective: The use of molecular genetic methods in pig breeding can significantly increase the efficiency of breeding and breeding work. We applied the Fst (fixsacion index) method, the main focus of the work was on the search for common options related to the number of born piglets and the weight of born piglets, since today the urgent task is to prevent a decrease in the weight of piglets at birth while maintaining high fertility of sows.Methods: One approach is to scan the genome, followed by an assessment of Fst and identification of selectively selected regions. We chose Large White sows (n = 237) with the same conditions of keeping and feeding. The data were collected from the sows across three farrowing. For genotyping, we used GeneSeek GGP Porcine HD Genomic Profiler v1, which included 68,516 single nucleotide polymorphisms evenly distributed with an average spacing of 25 kb (Illumina Inc, San Diego, CA, USA).Results: Based on the results of the Fst analysis, 724 variants representing selection signals for the signs BALWT, BALWT1, NBA, and TNB (weight of piglets born alive, average weight of the 1st piglets born alive, total number born alive, total number born). At the same time, 18 common variants have been identified that are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive characteristics in sows.Conclusion: Оur work resulted in identification of variants associated with the reproductive characteristics of pigs. Moreover, we identified, variants which are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive performance in sows.

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Section: Discussionmentioning

confidence: 99%

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

Romanets,

Bakoev,

Romanets

et al. 2024

Anim Biosci

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“…In any case, the conserved ROH island located on chromosome 14 could have had a key role in pig domestication since it was also identified in other breeds. In fact, the upstream region containing the AP1B1, EWSR1, KREMEN1, NEFH, THOC5, and ZNRF3 genes (see Table S3) was identified in Russian Large White pigs as a signature of selection associated with QTLs affecting reproduction and production traits [40], whereas the downstream region containing MORC2, SMTN, INPP5J, PLA2G3 and RNF185 genes (see Table S3) was identified by Li et al [41] as a signature of selection in Chinese pigs. This region is associated with a QTL affecting intramuscular fat linoleic acid content [42,43] that is positively correlated with pork flavor [44].…”

Section: Discussionmentioning

confidence: 99%

Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed

Gregorio

Perna

Trana

et al. 2023

Genes

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The recovery of Nero Lucano (NL) pigs in the Basilicata region (Southern Italy) started in 2001 with the collaboration of several public authorities in order to preserve native breeds that can play a significant economic role both due to their remarkable ability to adapt to difficult environments and the value of typical products from their area of origin. In this study, by using the Illumina Porcine SNP60 BeadChip, we compared the genetic structures of NL pigs reared in a single farm in two different periods separated by a time interval corresponding to at least three generations. The results showed an increase in the percentage of polymorphic loci, a decrease in the inbreeding coefficient calculated according to ROH genome coverage (FROH), a reduction in the number of ROH longer than 16 Mb and an increase in ROH with a length between 2 and 4 Mb, highlighting a picture of improved genetic variability. In addition, ROH island analysis in the two groups allowed us to identify five conserved regions, located on chromosomes 1, 4, 8, 14 and 15, containing genes involved in biological processes affecting immune response, reproduction and production traits. Only the conserved ROH island on chromosome 14 contains markers which, according to the literature, are associated with QTLs affecting thoracic vertebra number, teat number, gestation length, age at puberty and mean platelet volume.

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“…Анализируя информацию, представленную в российских и международных источниках, можно отметить важность исследования признаков плодовитости свиноматок (количество поросят при рождении и многоплодие) [7,8,9,10]. Тем не менее в последнее время, наряду с плодовитостью свиноматок, все более остро поднимаются вопросы о массе поросят при рождении [11,12,13,14]. С одной стороны, считают, что повышение количества поросят при рождении напрямую связано со снижением массы поросят.…”

Section: With the Intensive Increase In The Fertility Traits Of Sows ...unclassified

Search for genetic markers for selection and breeding aimed at increasing birth weight of piglets

Romanets,

Tretyakova

et al. 2023

Аграрная наука Евро-Северо-Востока

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With the intensive increase in the fertility traits of sows, the problem of decreasing the weight of piglets at birth has arisen. In this connection, the search for genetic variants associated with the birth weight of piglets is of particular relevance and scientific significance. The aim of the work was to identify genetic variants associated with piglet weight at birth and test them to select optimal genetic markers for selection and breeding work to improve reproductive performance of pigs on the basis of full genomic genotyping data using the Fst method. The studies were conducted in 2020-2022 on Large White pigs (n=239) bred at CJSC Plemzavod-Yubileiny in the Tyumen Region. Genotyping was performed using GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). Genomic data were filtered according to the following parameters --geno 0.1, -mind 0.1, -maf 0.05, -hwe 1e-7, --indep-pairwise 50 5 0.8. To identify genomic regions associated with piglet birth weight, there was used Fst statistics comparing genetic variants in pigs between two groups with high and low indices. Those in which the Fst values exceeded the quantile level of 0.999 were considered significant variants. Student's test was used to evaluate the significance of the effects of variant genotypes on the birth weight and number of piglets at birth. The results showed that there was a moderate negative relationship (-0.351) between piglet birth weight and number of piglets at birth. 17 SNPs associated with birth weight of piglets were identified, 9 of which were located in the KIF13A, STK24, FDFT1, ADGRD1, STX2, TMEM132D, ENSSSCG00000054866, ENSSSCG00000058459 genes, as well as SNPs rs81450496, rs80887103 in intergenic regions have been identified as promising genetic markers for increase in birth weight of piglets. The results obtained can be used to create domestic breeding technologies that improve the efficiency of pig breeding.

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Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Cited by 9 publications

References 45 publications

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed

Search for genetic markers for selection and breeding aimed at increasing birth weight of piglets

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