SNP discovery from next-generation transcriptome sequencing data and their validation using KASP assay in wheat (Triticum aestivum L.)

Chandra, Saket; Singh, Dharmendra; Pathak, Jyoti; Kumari, Supriya; Kumar, Manish; Poddar, Raju; Balyan, H. S.; Prabhu, K. V.; Gupta, P. K.; Mukhopadhyay, Kunal

doi:10.1007/s11032-017-0696-7

Cited by 19 publications

(15 citation statements)

References 60 publications

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“…Actually, the QTLs associating with yield and related traits in the salt stress field can play a more important role in the wheat breeding practices. Although, with the availability of next-generation sequencing, a large number of SNPs have recently been discovered in wheat [79]. Different types of high-throughput SNP arrays have been successfully used for studying marker-trait associations in wheat populations [79].…”

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

“…Although, with the availability of next-generation sequencing, a large number of SNPs have recently been discovered in wheat [79]. Different types of high-throughput SNP arrays have been successfully used for studying marker-trait associations in wheat populations [79]. However, the validation and utilization of these markers still represent major challenges owing to the time and labor required for genotyping huge progeny pools [79,80].…”

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

“…Different types of high-throughput SNP arrays have been successfully used for studying marker-trait associations in wheat populations [79]. However, the validation and utilization of these markers still represent major challenges owing to the time and labor required for genotyping huge progeny pools [79,80]. Recently, KASP genotyping technology was developed by LGC limited [81] for SNP genotyping.…”

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

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Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Zheng

Teng

et al. 2021

BMC Plant Biol

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Background Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. Result In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. Conclusion Utilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

show abstract

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Zheng

Teng

et al. 2021

BMC Plant Biol

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“…Genotyping technology has leapt forward during the past decade. The advent of next generation sequencing has supplied a large repository of Single Nucleotide Polymorphism (SNP) markers in wheat allowing high-density genotyping and QTL mapping [ 12 , 13 ]. High density genetic maps better identify and resolve QTL and SNP markers are preferred over other DNA markers, due to their abundance, high throughput and lower error rate [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

High density genetic mapping of Fusarium head blight resistance QTL in tetraploid wheat

et al. 2018

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Breeding for Fusarium head blight (FHB) resistance in durum wheat is complicated by the quantitative trait expression and narrow genetic diversity of available resources. High-density mapping of the FHB resistance quantitative trait loci (QTL), evaluation of their co-localization with plant height and maturity QTL and the interaction among the identified QTL are the objectives of this study. Two doubled haploid (DH) populations, one developed from crosses between Triticum turgidum ssp. durum lines DT707 and DT696 and the other between T. turgidum ssp. durum cv. Strongfield and T. turgidum ssp. carthlicum cv. Blackbird were genotyped using the 90K Infinium iSelect chip and evaluated phenotypically at multiple field FHB nurseries over years. A moderate broad-sense heritability indicated a genotype-by-environment interaction for the expression of FHB resistance in both populations. Resistance QTL were identified for the DT707 × DT696 population on chromosomes 1B, 2B, 5A (two loci) and 7A and for the Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B with the QTL on chromosome 1A and those on chromosome 5A being more consistently expressed over environments. FHB resistance co-located with plant height and maturity QTL on chromosome 5A and with a maturity QTL on chromosome 7A for the DT707 × DT696 population. Resistance also co-located with plant height QTL on chromosomes 2A and 3A and with maturity QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Additive × additive interactions were identified, for example between the two FHB resistance QTL on chromosome 5A for the DT707 × DT696 population and the FHB resistance QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Application of the Single Nucleotide Polymorphic (SNP) markers associated with FHB resistance QTL identified in this study will accelerate combining genes from the two populations.

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“…Actually, the QTL associating with yield and related traits in the salt stress eld may play key role in the wheat breeding practices. Although, with the availability of next-generation sequencing, a large number of SNPs have recently been discovered in wheat [79]. Different types of high-throughput SNP arrays have been successfully used for studying marker-trait associations in wheat populations [79].…”

Section: Development Of Molecular Markers For Marker-assisted Selectionmentioning

confidence: 99%

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Zheng

Luo

et al. 2020

Preprint

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Background Soil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield. Result In this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTL were significantly associated with traits under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14–50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding. Conclusion Utilizing a Wheat660K SNPs chip, QTL for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

show abstract

SNP discovery from next-generation transcriptome sequencing data and their validation using KASP assay in wheat (Triticum aestivum L.)

Cited by 19 publications

References 60 publications

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

High density genetic mapping of Fusarium head blight resistance QTL in tetraploid wheat

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

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