Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

Saxena, Maneesha S.; Bajaj, Deepak; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

doi:10.1371/journal.pone.0107484

Cited by 51 publications

(91 citation statements)

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“…Recently, LD studies have been performed in various plants, such as rice ( Oryza sativa L.) [19], barley ( Hordeum vulgare L.) [20], Maize ( Zea mays L.) [21], chickpea ( Cicer arietinum L.) [22], perennial ryegrass ( Lolium perenne L.) [23], and the model legume, Medicago truncatula [24]. The level of LD is constantly regarded as a standard to reflect mapping resolution.…”

Section: Introductionmentioning

confidence: 99%

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

et al. 2016

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BackgroundTo evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs.ResultsIn this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei’s gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 (P < 0.01).ConclusionsThe population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

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Section: Introductionmentioning

confidence: 99%

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

et al. 2016

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“…57, november-december 2017al., 2014a, 2014bBajaj et al, 2015;Van Oss et al, 2015) has been suggested to limit its capacity to tolerate stresses (Abbo et al, 2003). 57, november-december 2017al., 2014a, 2014bBajaj et al, 2015;Van Oss et al, 2015) has been suggested to limit its capacity to tolerate stresses (Abbo et al, 2003).…”

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Distinct Subgroups of Cicer echinospermum Are Associated with Hybrid Sterility and Breakdown in Interspecific Crosses with Cultivated Chickpea

et al. 2017

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Crop wild relatives are a reservoir of phenotypic variation not present in the germplasm of cultivated species and thus have great potential for crop improvement. However, issues of genetic compatibility often interfere with effective utilization of crop wild relative taxa. Among chickpea (Cicer arietinum L.) crop wild relatives, Cicer echinospermum P.H. Davis is the sole species in the secondary genepool, being partially compatible with the primary genepool that is composed of the cultigen and its progenitor wild species Cicer reticulatum Ladizinksy. We report results from genetic studies among interspecific hybrids between cultivated chickpea and accessions from six recently identified wild C. echinospermum sites in southeastern Turkey, encompassing the known genetic diversity of the secondary genepool. Our studies indicate that both hybrid sterility and hybrid breakdown occur and are associated with distinct subgroups of C. echinospermum. Analysis of early‐generation progenies suggests that both hybrid sterility and hybrid breakdown are conditioned by one to few genetic loci. These results clarify ambiguity in the nature of the hybridization barriers of reduced fertility in interspecific crossing of cultivated chickpea with C. echinospermum and should foster a more systematic and wider use of C. echinospermum for base broadening of cultivated chickpea.

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“…The amplified PCR fragments were purified, cloned and sequenced by an automated DNA sequencer (Applied Biosystems, ABI 3730xl DNA Analyzer, Vernon Hills, Illinois, USA). The high-quality sequences were aligned and compared among accessions, and SNPs were detected in diverse sequence components of orthologous chickpea genes following Kujur et al [24] and Saxena et al [34].…”

Section: Discovery and Genotyping Of Candidate Gene-derived Snpsmentioning

confidence: 99%

“…The population genetic structure among accessions was determined by a model-based program STRUCTURE v2.3.4 following Kujur et al [24,25] and Saxena et al [34]. The genome-wide and candidate gene-based genotyping data of SNPs physically mapped on eight kabuli chromosomes were analysed by PLINK and the full-matrix approach of TASSELv5.0 [34,37]. Based on these, the genome-wide LD patterns (r 2 , frequency correlation among pair of alleles across a pair of SNP loci) and LD decay (by plotting average r 2 against 50 and 20 kb uniform physical intervals across chromosomes) in population was determined.…”

Section: Phylogenetic Tree Construction Population Structure and Ld mentioning

confidence: 99%

“…For this, 20 of each low and high branch number-containing homozygous individuals along with parental accessions derived from two diverse inter-[C. arietinum desi ICC 4958 (BN: 25) × C. reticulatum wild ICC 17160 (BN: 17)] and intra-[C. arietinum desi ICC 12299 (BN: 29) × C. arietinum kabuli ICC 8261 (BN: 18)] specific F 7 RIL mapping populations were selected for DNA isolation. The BN-associated SNPs showing polymorphism between the parents of two mapping populations were genotyped in these homozygous mapping individuals using MALDI-TOF mass array SNP genotyping assay following Saxena et al [20,34]. Furthermore, the physical positions of BN-associated SNPs mapped on chromosomes were correlated with that of multiple BN QTLs identified/mapped previously on the inter-/intra-specific genetic linkage maps to validate these major genomic loci underlying BN QTLs in chickpea.…”

Section: Validation Of Trait-associated Snps In Bi-parental Mapping Pmentioning

confidence: 99%

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Identification of candidate genes for dissecting complex branch number trait in chickpea

et al. 2016

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a b s t r a c tThe present study exploited integrated genomics-assisted breeding strategy for genetic dissection of complex branch number quantitative trait in chickpea. Candidate gene-based association analysis in a branch number association panel was performed by utilizing the genotyping data of 401 SNP allelic variants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wide association study (GWAS) integrating both genome-wide GBS-(4556 SNPs) and candidate gene-based genotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli accessions (with 350-400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combined PVE) with branch number in chickpea. Of these, seven branch number-associated genes were further validated successfully in two inter (ICC 4958 × ICC 17160)-and intra (ICC 12299 × ICC 8261)-specific mapping populations. The axillary meristem and shoot apical meristem-specific expression, including differential up-and down-regulation (4-5 fold) of the validated seven branch number-associated genes especially in high branch number as compared to the low branch number-containing parental accessions and homozygous individuals of two aforesaid mapping populations was apparent. Collectively, this combinatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in seven potential known/candidate genes [PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1), BA1/LAX1 (BARREN STALK1/LIKE AUXIN1), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGA and Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth 2) and lipase] governing chickpea branch number. The useful information generated from this study have potential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars with more number of productive (pods and seeds) branches in chickpea.

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Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

Cited by 51 publications

References 80 publications

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers

Distinct Subgroups of Cicer echinospermum Are Associated with Hybrid Sterility and Breakdown in Interspecific Crosses with Cultivated Chickpea

Identification of candidate genes for dissecting complex branch number trait in chickpea

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