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Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat ( Triticum aestivum L.)
Targeted exome‐based genotype by sequencing (t‐GBS), a sequencing technology that tags SNPs and haplotypes in gene‐rich regions was used in previous genome‐wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty‐nine novel SNPs including 18 haplotypes for yield and yield‐compon...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435944/ https://www.ncbi.nlm.nih.gov/pubmed/37600239 http://dx.doi.org/10.1002/pld3.520 |
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author | Bhoite, Roopali Smith, Rosemary Bansal, Urmil Dowla, Mirza Bariana, Harbans Sharma, Darshan |
author_facet | Bhoite, Roopali Smith, Rosemary Bansal, Urmil Dowla, Mirza Bariana, Harbans Sharma, Darshan |
author_sort | Bhoite, Roopali |
collection | PubMed |
description | Targeted exome‐based genotype by sequencing (t‐GBS), a sequencing technology that tags SNPs and haplotypes in gene‐rich regions was used in previous genome‐wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty‐nine novel SNPs including 18 haplotypes for yield and yield‐components were identified. The present study aimed at developing SNP‐derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t‐GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m(−2), heads m(−2), and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1–37.6 in the FIGS population. High throughput PCR‐based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes—calcineurin B‐like‐ and dirigent protein, basic helix–loop–helix (BHLH‐), plant homeodomain (PHD‐) and helix–turn–helix myeloblastosis (HTH myb) type ‐transcription factor. Further, genome‐wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3′‐UTR, and intron) modifying gene expression and protein‐coding. This integrated approach of marker design for t‐GBS alleles, SNP functional annotation, and high‐throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs. |
format | Online Article Text |
id | pubmed-10435944 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-104359442023-08-19 Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat ( Triticum aestivum L.) Bhoite, Roopali Smith, Rosemary Bansal, Urmil Dowla, Mirza Bariana, Harbans Sharma, Darshan Plant Direct Research Articles Targeted exome‐based genotype by sequencing (t‐GBS), a sequencing technology that tags SNPs and haplotypes in gene‐rich regions was used in previous genome‐wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty‐nine novel SNPs including 18 haplotypes for yield and yield‐components were identified. The present study aimed at developing SNP‐derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t‐GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m(−2), heads m(−2), and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1–37.6 in the FIGS population. High throughput PCR‐based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes—calcineurin B‐like‐ and dirigent protein, basic helix–loop–helix (BHLH‐), plant homeodomain (PHD‐) and helix–turn–helix myeloblastosis (HTH myb) type ‐transcription factor. Further, genome‐wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3′‐UTR, and intron) modifying gene expression and protein‐coding. This integrated approach of marker design for t‐GBS alleles, SNP functional annotation, and high‐throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs. John Wiley and Sons Inc. 2023-08-18 /pmc/articles/PMC10435944/ /pubmed/37600239 http://dx.doi.org/10.1002/pld3.520 Text en © 2023 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Bhoite, Roopali Smith, Rosemary Bansal, Urmil Dowla, Mirza Bariana, Harbans Sharma, Darshan Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat ( Triticum aestivum L.) |
title | Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat (
Triticum aestivum
L.) |
title_full | Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat (
Triticum aestivum
L.) |
title_fullStr | Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat (
Triticum aestivum
L.) |
title_full_unstemmed | Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat (
Triticum aestivum
L.) |
title_short | Exome‐based new allele‐specific PCR markers and transferability for sodicity tolerance in bread wheat (
Triticum aestivum
L.) |
title_sort | exome‐based new allele‐specific pcr markers and transferability for sodicity tolerance in bread wheat (
triticum aestivum
l.) |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435944/ https://www.ncbi.nlm.nih.gov/pubmed/37600239 http://dx.doi.org/10.1002/pld3.520 |
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