Genome wide identification and characterization of the amino acid transporter (AAT) genes regulating seed protein content in chickpea (Cicer arietinum L.).

Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.

Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea.

KEY MESSAGE: Transcriptome landscape during early inflorescence developmental stages identified candidate flowering time regulators including Early Flowering 3a. Further genomics approaches validated the role of this gene in flowering time regulation. The early stages of inflorescence development in plants are as crucial as the later floral developmental stages. Several traits, such as inflorescence architecture and flower developmental timings, are determined during those early stages. In chickpea, diverse forms of inflorescence architectures regarding meristem determinacy and the number of flowers per node are observed within the germplasm. Transcriptome analysis in four desi chickpea accessions with such unique inflorescence characteristics identifies the underlying shared regulatory events leading to inflorescence development. The vegetative to reproductive stage transition brings about major changes in the transcriptome landscape. The inflorescence development progression associated genes identified through co-expression network analysis includes both protein-coding genes and long non-coding RNAs (lncRNAs). Few lncRNAs identified in our study positively regulate flowering-related mRNA stability by acting competitively with miRNAs. Bulk segregrant analysis and association mapping narrowed down an InDel marker regulating flowering time in chickpea. Deletion of 11 bp in first exon of a negative flowering time regulator, Early Flowering 3a gene, leads to early flowering phenotype in chickpea. Understanding the key players involved in vegetative to reproductive stage transition and floral meristem development will be useful in manipulating flowering time and inflorescence architecture in chickpea and other legumes.

Unraveling genetics of semi-determinacy and identification of markers for indeterminate stem growth habit in chickpea (Cicer arietinum L.).

Chickpea (Cicer arietinum L.) is predominantly an indeterminate plant and tends to generate vegetative growth when the ambient is conducive for soil moisture, temperature and certain other environmental conditions. The semi-determinate (SDT) types are comparatively early, resistant to lodging and found to be similar in their yield potential to indeterminate (IDT) lines. Indeterminate and semi-determinate genotypes are found to be similar during early stage, which makes it difficult to distinguish between them. Thus, there is a need to identify molecular markers linked either to indeterminate or semi-determinate plant types. The present study was carried out to study the genetics of semi-determinacy and identify molecular markers linked to stem growth habit. The study was undertaken in the cross involving BG 362(IDT) × BG 3078-1(SDT). All F1 plants were indeterminate, which indicates that indeterminate stem type is dominant over semi-determinate. In further advancement to F2 generation, F2 plants are segregated in the ratio of 3(Indeterminate): 1(Semi-determinate) that indicates that the IDT and SDT parents which are involved in the cross differed for a single gene. The segregation pattern observed in F2 is confirmed in F3 generation. The parental polymorphic survey was undertaken for molecular analysis using total of 245 SSR markers, out of which 41 polymorphic markers were found to distinguish the parents and were utilized for bulked segregant analysis (BSA). The segregation pattern in F2 indicates that the IDT (Indeterminate) and SDT (Semi-determinate) parents which are involved in the cross differed for single gene. The segregation pattern of F2 and F3 derived from the cross BG 362 (IDT) × BG 3078-1 (SDT) confirmed the genotypic structure of the newly found SDT genotype BG 3078-1 as dt1dt1Dt2Dt2. Three SSR markers TA42, Ca_GPSSR00560 and H3DO5 were found to be putatively linked to Dt1 locus regulating IDT stem growth habit. Our results indicate that the SSR markers identified for Dt1 locus helps to differentiate stem growth habit of chickpea in its early growth stage itself and can be efficiently utilized in Marker Assisted Selection (MAS) for changed plant type in chickpea.

Transcriptional signatures modulating shoot apical meristem morphometric and plant architectural traits enhance yield and productivity in chickpea.

Plant height (PH) and plant width (PW), two of the major plant architectural traits determining the yield and productivity of a crop, are defined by diverse morphometric characteristics of the shoot apical meristem (SAM). The identification of potential molecular tags from a single gene that simultaneously modulates these plant/SAM architectural traits is therefore prerequisite to achieve enhanced yield and productivity in crop plants, including chickpea. Large-scale multienvironment phenotyping of the association panel and mapping population have ascertained the efficacy of three vital SAM morphometric trait parameters, SAM width, SAM height and SAM area, as key indicators to unravel the genetic basis of the wide PW and PH trait variations observed in desi chickpea. This study integrated a genome-wide association study (GWAS); quantitative trait locus (QTL)/fine-mapping and map-based cloning with molecular haplotyping; transcript profiling; and protein-DNA interaction assays for the dissection of plant architectural traits in chickpea. These exertions delineated natural alleles and superior haplotypes from a CabHLH121 transcription factor (TF) gene within the major QTL governing PW, PH and SAM morphometric traits. A genome-wide protein-DNA interaction assay assured the direct binding of a known stem cell master regulator, CaWUS, to the WOX-homeodomain TF binding sites of a CabHLH121 gene and its constituted haplotypes. The differential expression of CaWUS and transcriptional regulation of its target CabHLH121 gene/haplotypes were apparent, suggesting their collective role in altering SAM morphometric characteristics and plant architectural traits in the contrasting near isogenic lines (NILs). The NILs introgressed with a superior haplotype of a CabHLH121 exhibited optimal PW and desirable PH as well as enhanced yield and productivity without compromising any component of agronomic performance. These molecular signatures of the CabHLH121 TF gene have the potential to regulate both PW and PH traits through the modulation of proliferation, differentiation and maintenance of the meristematic stem cell population in the SAM; therefore, these signatures will be useful in the translational genomic study of chickpea genetic enhancement. The restructured cultivars with desirable PH (semidwarf) and PW will ensure maximal planting density in a specified cultivable field area, thereby enhancing the overall yield and productivity of chickpea. This can essentially facilitate the achievement of better remunerative outputs by farmers with rational land use, therefore ensuring global food security in the present scenario of an increasing population density and shrinking per capita land area.