Global transcriptome and coexpression network analyses reveal cultivar‐specific molecular signatures associated with seed development and seed size/weight determination in chickpea

• Published in: The Plant journal : for cell and molecular biology 2017-09, Vol.91 (6), p.1088-1107
• Main Authors: Garg, Rohini, Singh, Vikash K., Rajkumar, Mohan Singh, Kumar, Vinay, Jain, Mukesh
• Format: Article
• Language: English
• Subjects: Cell division; Cicer - genetics; Cicer - growth & development; Cicer arietinum; coexpression network; Comparative analysis; Cultivars; Developmental stages; Embryogenesis; Embryonic growth stage; Endoreduplication; Gene expression; Gene Regulatory Networks; Gene sequencing; Genes; Genome, Plant - genetics; Germination; GSE79719; GSE79720; Maturation; Modules; Molecular modelling; Polymorphism, Single Nucleotide - genetics; Quantitative trait loci; Quantitative Trait Loci - genetics; seed development; seed size/weight; Seeds - genetics; Seeds - growth & development; Single-nucleotide polymorphism; Transcription; transcriptional modules; Transcriptome; transcriptome dynamics
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13621

Summary Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small‐seeded, Himchana 1 and large‐seeded, JGK 3). Our analysis identified stage‐specific expression for a significant proportion (>13%) of the genes in each cultivar. About one half of the total genes exhibited significant differential expression in JGK 3 as compared with Himchana 1. We found that different seed development stages can be delineated by modules of coexpressed genes. A comparative analysis revealed differential developmental stage specificity of some modules between the two cultivars. Furthermore, we constructed transcriptional regulatory networks and identified key components determining seed size/weight. The results suggested that extended period of cell division during embryogenesis and higher level of endoreduplication along with more accumulation of storage compounds during maturation determine large seed size/weight. Further, we identified quantitative trait loci‐associated candidate genes harboring single nucleotide polymorphisms in the promoter sequences that differentiate small‐ and large‐seeded chickpea cultivars. The results provide a valuable resource to dissect the role of candidate genes governing seed development and seed size/weight in chickpea. Significance Statement Deep sequencing reveals transcriptome dynamics and transcriptional regulatory network associated with seed development, and key factors that determine seed size/weight in chickpea.