Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

Wang, Dongxia; Cao, Dong; Zong, Yuan; Li, Yun; Wang, Jinmin; Li, Zongren; Liu, Baolong

doi:10.1080/13102818.2020.1857661

Cited by 7 publications

(2 citation statements)

References 32 publications

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“…Recently, QTL-seq was used in bread wheat to identify the candidate genomic region tightly linked to the awn inhibitor loci. Diagnostic markers were designed to understand the role of QTL in the awnless trait formation ( Wang et al, 2021 ). Moreover, this approach was applied to identify loci involved in tiller angle in bread wheat, which represents an important factor influencing yield.…”

Section: Current and Potential Methods To Identify And Clone Genes In...mentioning

confidence: 99%

Capturing Wheat Phenotypes at the Genome Level

et al. 2022

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Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

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Section: Current and Potential Methods To Identify And Clone Genes In...mentioning

confidence: 99%

Capturing Wheat Phenotypes at the Genome Level

et al. 2022

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“…The power of high-throughput whole-genome resequencing to identify genomic regions show contrasting results of an SNP index in the two bulk populations (each with 20-50 individuals) showing extreme phenotypes [209]. Recently QTL-seq was used in bread wheat to identify the candidate genomic region tightly linked to the awning inhibitor loci and diagnostic markers were designed to understand the role of QTL in the awnless trait formation [210]. Moreover, this approach was applied to identify loci involved in the tiller angle in bread wheat which represent an important factor influencing yield.…”

Section: Current and Potential Methods To Identify And Clone Genes In...mentioning

confidence: 99%

Wheat genomics and breeding: bridging the gap.

et al. 2021

View full text Add to dashboard Cite

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploid genome. However, an international public-private effort spanning nine years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat genome assembly in 2017. Shortly thereafter, in 2020, the genome of assemblies of additional fifteen global wheat accessions were released. Wheat has now entered into the pan-genomic era where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays capable of genotyping hundreds of wheat lines using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits including grain yield, yield-related traits, end-use quality and resistance to biotic and abiotic stresses. We also enlisted several reported candidate and cloned candidate genes responsible for the aforesaid traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits through the use of (i) clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) mediated gene-editing, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence.

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A large-effect QTL introgressed from ricebean imparts resistance to Mungbean yellow mosaic India virus in blackgram (Vigna mungo (L.) Hepper)

et al. 2022

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Until recently, precise location of genes and marker assisted selection was long thought in legumes such as blackgram due to lack of dense molecular maps. However, advances in next generation sequencing based high throughput genotyping technologies such as QTL-seq have revolutionized trait mapping in marker-orphan crops. Using QTL-seq approach, we have identi ed a large effect QTL for resistance to Mungbean yellow mosaic India virus (MYMIV) in blackgram variety Mash114. MYMIV is devastating disease responsible for huge yield losses in blackgram, greengram and other legumes. Mash114, a blackgram variety developed by Punjab Agricultural University, India showed consistent and high level of resistance to MYMIV since last nine years. Whole genome re-sequencing of MYMIV resistant and susceptible bulks derived from RILs of cross KUG253 X Mash114 identi ed a large effect QTL (qMYMIV6.1.1) spanning 3.4 Mbp on chromosome 6 explaining 70 per cent of total phenotypic variation.This region was further identi ed as an inter-speci c introgression from ricebean. The annotation of the introgressed segment suggested presence of clusters of disease resistance domains of which nine candidate genes were found to have role in virus resistance. Linkage mapping using KASP markers developed from these nine candidate genes identi ed the 500 kb genomic region equaling 1.9 cM on genetic map linked with MYMIV. The three KASP markers closely associated with MYMIV originated from serine threonine kinase, UBE2D2 and BAK1/ BRI1-ASSOCIATED RECEPTOR KINASE genes. These KASPs can be used for marker assisted transfer of introgressed segment into suitable backgrounds of Vigna species. Key MessageHere, we report identi cation of a large effect QTL conferring Mungbean yellow mosaic India virus resistance introgressed from ricebean in blackgram variety Mash114. The tightly linked KASP markers would assist in marker-assisted-transfer of this region into Vigna species infected by MYMIV.

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Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

Cited by 7 publications

References 32 publications

Capturing Wheat Phenotypes at the Genome Level

Capturing Wheat Phenotypes at the Genome Level

Wheat genomics and breeding: bridging the gap.

A large-effect QTL introgressed from ricebean imparts resistance to Mungbean yellow mosaic India virus in blackgram (Vigna mungo (L.) Hepper)

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