Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction

Takada, Luciana; Barbero, Marina Mortati Dias; Oliveira, Henrique Nunes de; Camargo, Gregório Miguel Ferreira de; Júnior, Gerardo Alves Fernandes; Aspilcueta-Borquis, Rusbel Raúl; Souza, Fernanda Fernandes; Boligon, Arione Augusti; Melo, Thaise Pinto de; Regatieri, Inaê Cristina; Feitosa, Fabieli Loise Braga; Fonseca, Larissa Fernanda Simielli; Magalhães, Ana Fabrícia Braga; Costa, Raphael Bermal; Albuquerque, Lúcia Galvão de

doi:10.1371/journal.pone.0190197

Cited by 16 publications

(9 citation statements)

References 62 publications

(69 reference statements)

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“…This region harbors PLAG1 and XKR4 genes. The XKR4 was associated with subcutaneous rump fat thickness, scrotal circumference, serum concentration of prolactin, and sexual precocity (Fortes et al, 2012a;Porto Neto et al, 2012;Bastin et al, 2014;Takada et al, 2018). PLAG1 has been implicated in the regulation of stature and weight (Littlejohn et al, 2012;Pryce et al, 2012;Song et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

et al. 2020

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Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

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Section: Discussionmentioning

confidence: 99%

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

et al. 2020

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“…XKR4 gene associated with feed intake and growth traits (Lindholm-Perry et al, 2012), meat and carcass (Bolormaa et al, 2011; Porto Neto et al, 2012) and reproductive traits (Fortes et al, 2012; Takada et al, 2018) has been repeatedly detected to be under strong selection in composite cattle (Bahbahani et al, 2015; Taye et al, 2017; Yurchenko et al, 2018). In this study, the most significant SNP under selection (BTB-01532239) is located at position 24437778 on BTA 14 (| iHS| = -6.84, p -value = 7.8 × 10 -22 ), suggesting a strong sweep for the derived allele (Voight et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

Signatures of Selection in Admixed Dairy Cattle in Tanzania

et al. 2018

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Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.

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“…Takada and others focused on haplotypes encompassing 125 candidate genes and identified nine haplotypes with significant association with early pregnancy. Those haplotypes were located in the genes pregnancy-associated plasma protein-A2 ( PAPP-A2 ), estrogen-related receptor gamma ( ESRRG ), pregnancy-associated plasma protein-A ( PAPP-A ), kell blood group complex subunit-related family ( XKR4 ), and mannose-binding lectin ( MBL-1 ) [ 88 ].…”

Section: Current and Emerging Technologies For Assessing Fertility Inmentioning

confidence: 99%

Beef heifer fertility: importance of management practices and technological advancements

Moorey

Biase

2020

J Animal Sci Biotechnol

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The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA, National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program. The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers. There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.

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Genomic association for sexual precocity in beef heifers using pre-selection of genes and haplotype reconstruction

Cited by 16 publications

References 62 publications

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

Signatures of Selection in Admixed Dairy Cattle in Tanzania

Beef heifer fertility: importance of management practices and technological advancements

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