Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Mishra, Dwijesh Chandra; Sikka, P.; Yadav, Sunita; Bhati, Jyotika; Paul, Souvik; Adnot, Jérôme; Singh, Inderjeet; Nath, Abhigyan; Budhlakoti, Neeraj; Rao, Atmakuri Ramakrishna; Rai, Anil; Chaturvedi, Krishna Kumar

doi:10.1016/j.ygeno.2020.04.012

Cited by 18 publications

(12 citation statements)

References 42 publications

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“…This lower number of SNPs in genic region was also reported in water buffalo targeted sequencing in the Jafarabadi breed (84). In another study of the Murrah water buffalo breed, genic region SNPs (79.40%) were found in nearly one-fifth of non-genic region SNPs (19.26%) in terms of their relative abundance (85). Though exonic variations are very limited in number, they do play an important role in population differentiation at the genetic level (86).…”

Section: Evaluation Of Mastitis Tgp Based Variant Mining (Snps and Indels)supporting

confidence: 60%

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

et al. 2021

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Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

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Section: Evaluation Of Mastitis Tgp Based Variant Mining (Snps and Indels)supporting

confidence: 60%

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

et al. 2021

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“…From functional annotation of breed-wise SNP/InDels, 12326/8469, 15152/2044, 4798/1100, and 21762/17222 genes were found to have abundance of SNPs/InDels in Bangladesh, Egyptian, Jaffrabadi, and Murrah breeds, respectively ( Figure 2C for SNPs and Figure 2D for InDels). SNP discovery plays an important role in obtaining varying alleles associated with different traits of interest ( Mishra et al, 2020 ). This can be useful in marker trait association studies for various traits ( Pareek et al, 2008 ).…”

Section: Resultsmentioning

confidence: 99%

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

et al. 2022

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Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.

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“…This gene has been reported to be associated with immunity and growth traits in cattle ( Abo-Ismail et al, 2017 ). CNTNAP2 gene is also reported to play an important role in milk synthesis pathway in water buffalo ( Mishra et al, 2020 ). These positively selected genes may create the observed differences in the Murrah buffaloes from the rest of the buffalo breeds included in the study and makes the Murrah as one of the high milk-producing buffalo breed with high fertility and immunity.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, Dutta et al (2020) identified selection sweeps in seven Indian riverine buffaloes and compared patterns of between-species selective sweeps with different cattle breeds using whole-genome sequencing (WGS) data. Since WGS is a costly process, several workers have proposed reduced representation genotyping techniques such as the double digest restriction site-associated DNA sequencing (ddRAD-seq) as a useful alternative to WGS for genotyping Indian buffaloes ( Surya et al, 2019 ; Mishra et al, 2020 ). For the present study, the genotype data of six Indian buffalo breeds (Murrah, Surti, Mehsana, Bhadawari, Pandharpuri, and Toda) was generated using ddRAD sequencing.…”

Section: Introductionmentioning

confidence: 99%

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

et al. 2021

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India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and FST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and FST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.

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Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Cited by 18 publications

References 42 publications

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis)

Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India

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