Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean

Jiang, Song; Li, Zhen; Liu, Zhangxiong; Guo, Yong; Qiu, Lijuan

doi:10.3389/fpls.2017.00919

Cited by 106 publications

(84 citation statements)

References 57 publications

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“…However, maize geneticists are actively working to identify the modifiers in contrasting genetic backgrounds (Bolduc et al 2014) . In these cases, conventional BSA-Seq could be used to identify both causative lesions and modifiers in one step (Song et al 2017) .…”

Section: Discussionmentioning

confidence: 99%

“…The most important advantage of BSA-Seq is its simplicity, both in terms of sample collection and data analysis. While BSA-Seq is used extensively in other taxa (Schneeberger and Weigel 2011;Abe et al 2012;Mascher et al 2014;Woods et al 2014;Ding et al 2017;Song et al 2017;Jiao et al 2018) , gene mapping via Bulked-Segregant RNA-Seq (BSR-Seq) is more often used for cloning maize genes (Liu et al 2012;Li et al 2013;Nestler et al 2014;Tang et al 2014) . In BSR-Seq, RNA from a pool of mutants and RNA from a pool of non-mutants is used to make RNA-Seq libraries (Liu et al 2012) .…”

Section: Discussionmentioning

confidence: 99%

“…This modification to BSA-Seq has been called MutMap (Abe et al 2012) . BSA-Seq has been used to identify mutant loci in Arabidopsis thaliana , soybean, barley, Mimulus, rice, sorghum, and Brachypodium distachyon (Schneeberger and Weigel 2011;Abe et al 2012;Mascher et al 2014;Woods et al 2014;Ding et al 2017;Song et al 2017;Jiao et al 2018) . Although BSA-Seq has been used to identify genomic regions underlying variation in flowering time and plant height QTLs in a maize population (Haase et al 2015) , there have been no reports of it used to clone mutant maize genes.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

Klein

Xiao

Conklin

et al. 2018

Preprint

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Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1, and to identify a new allele of defective kernel1. Our method provides a quick, simple way to clone genes in maize.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

Klein

Xiao

Conklin

et al. 2018

Preprint

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“…one bulk has more allele A while the other bulk has more allele a. BSA was primarily used to develop genetic markers for detecting gene-trait association at its early stage (1,2). Application of the next generation sequencing (NGS) technology to BSA eliminated the time-consuming and labor-intensive marker development and genetic mapping steps, and dramatically sped up the detection of gene-trait associations (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). This technique was termed either QTL-seq or BSA-Seq in different publications (5,6,19), we adapted the latter here because it can be applied to study both qualitative and quantitative traits.…”

Section: Introductionmentioning

confidence: 99%

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

Zhang

Panthee

2019

Preprint

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Bulked segregant analysis (BSA), coupled with next generation sequencing (NGS), allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect major single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost. Here we developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python, the program was named PyBSASeq. Using PyBSASeq, the likely trait-associated SNPs (ltaSNPs) were identified via Fisher's exact test and then the ratio of the ltaSNPs to total SNPs in a chromosomal interval was used to identify the genomic regions that condition the trait of interest. The results obtained this way are similar to those generated by the current methods, but with more than five times higher sensitivity, which can reduce the sequencing cost by~80% and makes BSA-Seq more applicable for the species with a large genome.

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“…Other strategies such as bulked segregant analysis (BSA) may also be useful. When BSA is coupled to more recent next generation sequencing (NGS) technologies, it provides a fast and easy method for identifying molecular markers tightly linked to the causal gene/s underlying a given phenotype (Song et al 2017). A segregating population from a genetic cross is developed, then the individuals are assayed for the focal trait and two pools (bulks) of segregants are created by selecting individuals from the tails of the phenotypic distribution (Magwene et al 2011).…”

Section: General Discussion and Future Directionmentioning

confidence: 99%

Creating a new allohexaploid Brassica crop:determination of fertility and stability in novel Brassica hybrids

Mwathi¹

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The Brassica genus is an economically important group of diploid (single genome) and allotetraploid (two-genome) species used as oilseeds, vegetables and condiments. Although no allohexaploid (three-genome) Brassica species exists in nature, the production of an allohexaploid Brassica crop could be beneficial for agriculture. However, production of a stable and fertile Brassica allohexaploid is currently hindered by challenges of infertility and unstable meiosis. To date, incremental progress has been made in creating an allohexaploid species using several different species combinations. Despite this, a gap in knowledge currently exists for genomic stability among Brassica allohexaploids, critical in the establishment of a successful species. Firstly, I investigated fertility and meiotic stability in 100 plants from the cross B. carinata × B. rapa (A2 allohexaploid population) and 69 plants from the cross (B. napus × B. carinata) × B. juncea (H2 allohexaploid population). Estimated pollen viability, self-pollinated seed set, number of seeds on the main shoot, number of pods on the main shoot, seeds per 10 pods and plant height were measured for both the A2 and H2 populations and a set of reference control cultivars. The H2 population had high segregation for pollen viability and meiotic stability, while the A2 population was characterised by low pollen fertility and a high level of chromosome loss. Both populations were taller, but had lower average fertility trait values, than the control cultivar samples. Additionally, I established that the genotypes of the parents and H1 hybrids are affecting chromosome pairing and fertility phenotypes in the H2 population. Next, I investigated fertility, meiosis and genetic variability in sets of self-pollinated progenies (the MDL2 population) resulting from first generation microspore-derived plants (the MDL1 population). These populations were derived from microspores of a near-allohexaploid interspecific hybrid plant from the cross (Brassica napus × B. carinata) × B. juncea. Fertility decreased from MDL1 to MDL2 population, with several fixed chromosome duplications and deletions present as well as novel genomic events seen to have occurred from the MDL1 to MDL2. Genetic non-identity between lines within various progeny sets in MDL2 was also observed, uncharacteristic of what would be expected of a microspore-derived (normally doubled haploid; DH) population. iii Finally, I made novel interspecific hybrids between wild C genome species, B. oleracea and B. juncea to utilise this germplasm for the creation of a diverse allohexaploid species. Hand pollinations between two genotypes of B. juncea (Xingyou 4 and B578) and B. oleracea (TO1000) and wild C genome species B. incana, B. montana and B. cretica were performed (747 total bud pollinations, average 62.25 per cross combination) in both cross directions. The combination with B. oleracea produced six triploid hybrids (2n = ABC) from 85 flower pollinations. Pollen fertility in triploid hybrids was low; between 2 -10% (averag...

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Next-Generation Sequencing from Bulked-Segregant Analysis Accelerates the Simultaneous Identification of Two Qualitative Genes in Soybean

Cited by 106 publications

References 57 publications

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

Creating a new allohexaploid Brassica crop:determination of fertility and stability in novel Brassica hybrids

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