Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation.
Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To link the genome sequence information with agronomic traits resulting from specific developmental processes, a Cajanus cajan gene expression atlas (CcGEA) was developed using the Asha genotype. Thirty tissues/organs representing developmental stages from germination to senescence were used to generate 590.84 million paired-end RNA-Seq data. The CcGEA revealed a compendium of 28 793 genes with differential, specific, spatio-temporal and constitutive expression during various stages of development in different tissues. As an example to demonstrate the application of the CcGEA, a network of 28 flower-related genes analysed for cis-regulatory elements and splicing variants has been identified. In addition, expression analysis of these candidate genes in male sterile and male fertile genotypes suggested their critical role in normal pollen development leading to seed formation. Gene network analysis also identified two regulatory genes, a pollen-specific SF3 and a sucrose-proton symporter, that could have implications for improvement of agronomic traits such as seed production and yield. In conclusion, the CcGEA provides a valuable resource for pigeonpea to identify candidate genes involved in specific developmental processes and to understand the well-orchestrated growth and developmental process in this resilient crop.
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.
Lekha T
LT
Pazhamala
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.
Shilp
S
Purohit
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.
Rachit K
RK
Saxena
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.
Vanika
V
Garg
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.
L
L
Krishnamurthy
INRA - Research Institute in Horticulture and Seeds (IRHS), 49071 Beaucouze, France.
Jerome
J
Verdier
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, India.|School of Plant Biology and Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
Rajeev K
RK
Varshney
D036561:Cajanus / Q000235:genetics* / Q000502:physiology; D018556:Crops, Agricultural / Q000235:genetics* / Q000502:physiology; D005298:Fertility / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000502:physiology*; D054817:Pollination / Q000235:genetics* / Q000502:physiology; D012639:Seeds / Q000235:genetics* / Q000502:physiology
Cajanus cajan; CcGEA; gene clustering; gene expression atlas; gene networking; legume genomics; male sterile genotype; pigeonpea; pollen-specific SF3; sucrose–proton symporter.