Systematic analyses for candidate genes of milk production traits in water buffalo (<i>Bubalus Bubalis</i>)

Du, Chao; Deng, Tingxian; Zhou, Yan; Ye, T.; Zhou, Zhuqing; Zhang, Sheng; Shao, Bin; Wei, Pengfei; Sun, Hui; Khan, Faheem Ahmed; Yang, Liguo; Hua, Guo

doi:10.1111/age.12739

Cited by 49 publications

(28 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For instance, the selection signature region on BTA17 overlaps with a QTL that harbours 4 candidate genes ( BRI3BP, DHX37, UBC, SCARB1 ) associated with carcass trait (marbling) in cattle (Lee et al, 2012). Similarly, two candidate genes ( ANKH and CTNND2 ) related with milk production traits (Du et al, 2019; Sanchez et al, 2017) were mapped within two significant regions on BTA20.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

Mastrangelo

Jemaa

Ciani

et al. 2020

J Animal Breeding Genetics

View full text Add to dashboard Cite

The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least two approaches in VPR, VPN and VCA, respectively. Most of these candidate regions were population-specific but we found one common genomic region spanning 2.38 Mb on BTA06 which either overlaps or is located close to runs of homozygosity islands detected in the three populations. This region included inter alia two well-known genes: KDR, a well-established coat colour gene, and CLOCK, which plays a central role in positive regulation of inflammatory response and in the regulation of the mammalian circadian rhythm. The other candidate regions identified harboured genes associated mainly with milk and meat traits as well as genes involved in immune response/inflammation or associated with behavioural traits. This last category of genes was mainly identified in VCA, which is selected for fighting ability. Overall, our results provide, for the first time, a glimpse into regions of the genome targeted by selection in Valdostana cattle. Finally, this study illustrates the relevance of using multiple complementary approaches to identify genomic regions putatively under selection in livestock.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

Mastrangelo

Jemaa

Ciani

et al. 2020

J Animal Breeding Genetics

View full text Add to dashboard Cite

show abstract

“…Recently, candidate genes harboring single nucleotide polymorphisms (SNP) significantly associated with milk fat content (Li et al, 2018c;Gu et al, 2019), protein percentage (Manzoor et al, 2018(Manzoor et al, , 2020, and fatty acid composition (Cosenza et al, 2017(Cosenza et al, , 2018 have been identified on different buffalo chromosomes. As for milk yield, one of the most important economic traits in buffalo industry, associated polymorphisms have been identified at the whole genome level (Wu et al, 2013;Venturini et al, 2014;de Camargo et al, 2015;Menon et al, 2016;El-Halawany et al, 2017;Iamartino et al, 2017;da Costa Barros et al, 2018;Du et al, 2019). These studies have made great contributions to the progress of various breeding programs in buffalo.…”

Section: Introductionmentioning

confidence: 99%

Identification of candidate genes associated with milk yield trait in buffaloes ( Bubalus bubalis ) by restriction-site-associated DNA sequencing

et al. 2020

Revista Brasileira De Zootecnia

View full text Add to dashboard Cite

Breeding and genetics Full-length research article Identification of candidate genes associated with milk yield trait in buffaloes (Bubalus bubalis) by restriction-site-associated DNA sequencing ABSTRACT-The objectives of our present study included the screening of single nucleotide polymorphisms (SNP) that show significant differences in allelic frequencies between two buffalo populations (Egyptian and Chinese buffaloes), categorization of functional genes associated with these SNP by gene ontology, and pathway analyses to further understand their potential values as candidate genes closely associated with milk yield trait in buffaloes. In this study, double digest restrictionsite associated DNA sequencing was performed on Illumina HiSeq 2500 platform for 20 and 25 female buffaloes from Egypt and China, respectively. Approximately 118 Gb of sequencing data were obtained, and a total of 110,129 and 150,535 putative SNP were detected in Egyptian and Chinese buffaloes, respectively. Focused only on those SNP that differed significantly in allelic frequencies between the two populations, we found that genes associated with these SNP were significantly over-represented in the ionotropic glutamate receptor pathway, the endothelin signaling pathway, and the gonadotropin-releasing hormone receptor pathway, which contained a total of 29 genes. Of these, nine genes (ADCY5, CACNA1A, CREB1, INHBA, INHBB, PIK3R1, PLCB1, PRKCE, and SMAD2) participating in the hormonal regulation of lactation, were considered to be promising candidate genes worthy of further investigations for favorable alleles associated with milk yield. Our results provide useful information about genetic variations in Egyptian and Chinese buffaloes. The potential influences of nine candidate genes and their associated SNP on milk yield need to be validated in more buffalo populations.

show abstract

“…This finding suggests that the candidate gene may contribute to milk metabolic pathways. Many studies have reported the kelch-like family member 29 (Gene ID: S12_75087502) involved in growth [89] and milk production in dairy cattle and buffalos [78,90,91]. Recently, it was also identified as the closest gene mapped by novel QTL-lead SNP for milking speed in French Holstein cattle, and T was an effect allele with a −0.08 allelic substitution effect of the SNP [92].…”

Section: Plos Onementioning

confidence: 99%

“…Multidrug resistance-associated protein 4-like (Gene ID: S13_18088155) is a member of C subfamily of ATP-binding cassette (ABC) transporters. ABCC4 acts in basic metabolic pathways and is highly polymorphic, with potential effects in a variety of phenotypes, and has also been detected in milk during early lactation [74,91,[93][94][95]. The genetic effects of ABCG2 polymorphism have been observed for milk yield traits in Chinese Holstein cattle [96,97].…”

Section: Plos Onementioning

confidence: 99%

Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

et al. 2020

View full text Add to dashboard Cite

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.

show abstract

Systematic analyses for candidate genes of milk production traits in water buffalo (Bubalus Bubalis)

Cited by 49 publications

References 29 publications

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

Genome‐wide detection of signatures of selection in three Valdostana cattle populations

Identification of candidate genes associated with milk yield trait in buffaloes ( Bubalus bubalis ) by restriction-site-associated DNA sequencing

Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight

Contact Info

Product

Resources

About