A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200–250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34 % combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6–27.3 % PVE at 5.4–11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41 % combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea

Deciphering the Genetic Architecture of Cooked Rice Texture

The textural attributes of cooked rice determine palatability and consumer acceptance. Henceforth, understanding the underlying genetic basis is pivotal for the genetic improvement of preferred textural attributes in breeding programs. We characterized diverse set of 236 Indica accessions from 37 countries for textural attributes, which includes adhesiveness (ADH), hardness (HRD), springiness (SPR), and cohesiveness (COH) as well as amylose content (AC). A set of 147,692 high quality SNPs resulting from genotyping data of 700K high Density Rice Array (HDRA) derived from the Indica diversity panels of 218 lines were retained for marker-trait associations of textural attributes using single-locus (SL) genome wide association studies (GWAS) which resulted in identifying hotspot on chromosome 6 for AC and ADH attributes. Four independent multi-locus approaches (ML-GWAS) including FASTmrEMMA, pLARmEB, mrMLM, and ISIS_EM-BLASSO were implemented to dissect additional loci of major/minor effects influencing the rice texture and to overcome limitations of SL-based GWAS approach. In total 224 significant quantitative trait nucleotide (QTNs) were identified using ML-GWAS, of which 97 were validated with at least two out of the four multi-locus methods. The GWAS results were in accordance with the very significant negative correlation (r = −0.83) observed between AC and ADH, and the significant correlation exhibited by AC (r < 0.4) with HRD, SPR, and COH. The novel haplotypes and putative candidate genes influencing textural properties beyond AC will be a useful resource for deployment into the marker assisted program to capture consumer preferences influencing rice texture and palatability

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

<div><p>Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated <i>Cicer</i> accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.</p></div

Microsatellite and SNP marker-based assessment of population genetic structure among wild and cultivated chickpea.

<p>Optimization of population structure with varying population number K = 5 to K = 7 and their inferred best possible population genetic structure for 94 cultivated and wild <i>Cicer</i> accessions using 334 genic and 144 genomic microsatellite markers and 380 TF gene-derived SNP markers physically mapped across eight chromosomes. These mapped markers assigned 94 accessions into six population that majorly grouped accordingly by their species and gene pools of origination. The accessions represented by vertical bars along the horizontal axis were classified into K colour segments based on their estimated membership fraction in each K cluster. Six diverse colours represent different population groups based on optimal population number K = 6.</p

SNP marker-based genotypic variation among wild and cultivated chickpea.

<p>Call cluster plots for two representative SNP loci (C/T) demonstrating the genotyping information of all 94 cultivated and wild <i>Cicer</i> accessions assayed with MALDI-TOF mass array. Distinct differentiation of homozygous and heterozygous SNPs based on mass differences of corresponding alleles are evident.</p

Some passport information on global wild and cultivated annual <i>Cicer</i> accessions used in the present study.

<p>Some passport information on global wild and cultivated annual <i>Cicer</i> accessions used in the present study.</p

Microsatellite marker-based genotypic variation among wild and cultivated chickpea.

<p>Allelic variation detected among a representative set of cultivated and wild accessions belonging to seven <i>Cicer</i> species using normal unlabeled and fluorescent dye-labelled genic and genomic microsatellite markers by gel-based assay (A) and automated fragment analyzer (B), respectively. A maximum of 13 polymorphic alleles were amplified by markers among 94 accessions using the gel-based assay and automated fragment analyzer. The fragment sizes (bp) for all the alleles are indicated. M: 50 bp DNA size standard.</p

Microsatellite and SNP marker-based genetic diversity and phylogeny among wild and cultivated chickpea.

<p>Unrooted phylogenetic tree depicting the genetic relationships among 94 cultivated and wild accessions belonging to seven <i>Cicer</i> species based on Nei's genetic distance using 334 genic and 144 genomic microsatellite markers and 380 TF gene-derived SNP markers. Molecular classification clearly differentiated 94 accessions into six different clusters, which corresponds to their species and gene pools of origination. Percentages of confidence obtained in bootstrap analysis are indicated at the corresponding node for each cluster.</p

Microsatellite and SNP marker-based estimation of genome-wide and population-specific LD patterns in wild chickpea.

<p>(A) Estimates of LD (mean r²) for linked, unlinked and global markers (478 genic and genomic microsatellite markers and 380 TF gene-based SNP markers). The bar indicates the standard error. *ANOVA significance at p<0.01. (B) LD decay (mean r²) in six population groups as defined by population genetic structure. For LD decay, the r² value of marker physical distance of 0 kb is considered as 1. The marked dots indicate the mean r² values for marker intervals of 0–200, 200–400, 400–600, 600–800, 800–1000 and 1000–1200 kb, respectively. The curve was drawn across the dots using non-linear regression model. “All” includes the LD estimates and decay across entire six population groups.</p