Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize

Quarrie, S. A.; Lazic-Jancic, Vesna; Kovačević, Dragan; Steed, Andy; Pekic, S.

doi:10.1093/jxb/50.337.1299

Cited by 126 publications

(82 citation statements)

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“…In both studies, bulked segregant analysis (BSA), followed by mapping of the markers displaying significant associations with the trait, was applied. Although this approach allows the identification of genomic regions that have major effects on the trait, a thorough QTL analysis is necessary to obtain a more general overview of the genetic factors determining resistance and to identify additional genomic regions with minor effects (Quarrie et al, 1999). An essential step for QTL analysis is the construction of a detailed linkage map of the population used for phenotypic analysis.…”

Section: Introductionmentioning

confidence: 99%

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Muylle¹,

Baert²,

Bockstaele

et al. 2005

Heredity

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Crown rust resistance is an important selection criterion in ryegrass breeding. The disease, caused by the biotrophic fungus Puccinia coronata, causes yield losses and reduced quality. In this study, we used linkage mapping and QTL analysis to unravel the genomic organization of crown rust resistance in a Lolium perenne population. The progeny of a pair cross between a susceptible and a resistant plant were analysed for crown rust resistance. A linkage map, consisting of 227 loci (AFLP, SSR, RFLP and STS) and spanning 744 cM, was generated using the two-way pseudo-testcross approach from 252 individuals. QTL analysis revealed four genomic regions involved in crown rust resistance. Two QTLs were located on LG1 (LpPc4 and LpPc2) and two on LG2 (LpPc3 and LpPc1). They explain 12.5, 24.9, 5.5 and 2.6% of phenotypic variance, respectively. An STS marker, showing homology to R genes, maps in the proximity of LpPc2. Further research is, however, necessary to check the presence of functional R genes in this region. Synteny at the QTL level between homologous groups of chromosomes within the Gramineae was observed.LG1 and LG2 show homology with group A and B chromosomes of oat on which crown rust-resistance genes have been identified, and with the group 1 chromosomes of the Triticeae, on which leaf rustresistance genes have been mapped. These results are of major importance for understanding the molecular background of crown rust resistance in ryegrasses. The identified markers linked to crown rust resistance have the potential for use in marker-assisted breeding. Heredity (2005) 95, 348-357.

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Section: Introductionmentioning

confidence: 99%

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Muylle¹,

Baert²,

Bockstaele

et al. 2005

Heredity

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“…Similar studies have been performed by Quarrie et al (1999) using BSA and by grouping plants into either high or poorly cold tolerance-specific expression groups according to their particular traits of drought resistance. In another study, Kumar et al (2014) used BSA to assess high yielding drought tolerance in rice.…”

Section: Discussionmentioning

confidence: 87%

“…Until recently, many studies have had to rely on BSA using genetic stocks differing in expression of a particular trait to test the association between the agronomic traits and molecular markers (Quarrie et al, 1999;Fernández-Del-Carmen et al, 2007;Becker et al, 2011;Deschamps et al, 2012;Ye et al, 2015). Populations such as BSA are more easily prepared to identify plants or lines with high or low expression of the trait of interest.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, two sets of DNA can be prepared in only a few months, one from the 'high' individuals and the other from the 'low' individuals, and analyzed for allele frequency of molecular markers. BSA has been used previously to discover tolerance mechanisms in maize inbred lines (Quarrie et al, 1999). The major advantages of using BSA include the detection of QTLs from large populations, extreme mapping from disparate ends of a phenotypic range in a population, and the use of near-isogenic lines in specific regions of the genome (Michelmore et al, 1991;Deschamps et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

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Bulk segregant analysis (BSA) for improving cold stress resistance in maize using SSR markers

Farooqi¹,

J²,

Hong

et al. 2016

Genet. Mol. Res.

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ABSTRACT. In this study, eight inbred maize lines with high or low tolerance to cold temperature were investigated using bulk segregant analysis (BSA). Genetic diversity and genetic relationships were investigated using 100 simple sequence repeat (SSR) markers linked to cold tolerance in maize. A total of 319 alleles were identified. Among these, 128 were high coldtolerant-specific alleles and 61 were poorly coldtolerant-specific alleles, while the remaining 130 were shared between the two types. The number of alleles per locus ranged from 2 to 5, with an average of 3.19. The major allele frequency varied from 0.39 to 0.53 with an average of 0.47. The average gene diversity and polymorphic information content among all lines were 0.63 and 0.58, respectively. A dendrogram analysis identified three main clusters and most of the high tolerant inbred lines were clearly distinguished from the poorly tolerant inbred lines. In addition to the BSA, a total of 84 SSR markers were identified as high cold tolerance-specific alleles and 52 SSRs were detected as poorly cold tolerance-specific alleles. Of these, bnlg1273, umc1124, dupssr21, mmc0251, mmc0181, and phi041 have great potential for being molecular markers for cold tolerance in maize. Our results were in agreement with results previously reported for SSR markers linked with cold tolerance in maize. The identification and characterization of high and poorly cold tolerant maize lines based on SSR markers will be useful for future maize breeding studies.

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“…Selective genotype data for progeny with one of the two extreme phenotypes have been found to be most informative (Lander and Botstein 1989). Individuals can be genotyped separately via single segregant analysis (SSA) or by pooling their genomic DNA and performing bulk segregant analysis (BSA) (Arnheim et al 1985;Michelmore et al 1991;Quarrie et al 1999). Once a QTL has been located in the genome, the next level of analysis is the identification of the responsible QTG and QTN, which are typically verified by the homologous replacement of the candidate gene or polymorphism between both parental strains using site-directed mutagenesis (Sinha et al 2008b).…”

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confidence: 99%

Oxidative Stress Survival in a Clinical Saccharomyces cerevisiae Isolate Is Influenced by a Major Quantitative Trait Nucleotide

Diezmann

Dietrich

2011

Genetics

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One of the major challenges in characterizing eukaryotic genetic diversity is the mapping of phenotypes that are the cumulative effect of multiple alleles. We have investigated tolerance of oxidative stress in the yeast Saccharomyces cerevisiae, a trait showing phenotypic variation in the population. Initial crosses identified that this is a quantitative trait. Microorganisms experience oxidative stress in many environments, including during infection of higher eukaryotes. Natural variation in oxidative stress tolerance is an important aspect of response to oxidative stress exerted by the human immune system and an important trait in microbial pathogens. A clinical isolate of the usually benign yeast S. cerevisiae was found to survive oxidative stress significantly better than the laboratory strain. We investigated the genetic basis of increased peroxide survival by crossing those strains, phenotyping 1500 segregants, and genotyping of high-survival segregants by hybridization of bulk and single segregant DNA to microarrays. This effort has led to the identification of an allele of the transcription factor Rds2 as contributing to stress response. Rds2 has not previously been associated with the survival of oxidative stress. The identification of its role in the oxidative stress response here is an example of a specific trait that appears to be beneficial to Saccharomyces cerevisiae when growing as a pathogen. Understanding the role of this fungal-specific transcription factor in pathogenicity will be important in deciphering how fungi infect and colonize the human host and could eventually lead to a novel drug target.

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Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize

Cited by 126 publications

References 12 publications

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Bulk segregant analysis (BSA) for improving cold stress resistance in maize using SSR markers

Oxidative Stress Survival in a Clinical Saccharomyces cerevisiae Isolate Is Influenced by a Major Quantitative Trait Nucleotide

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