APETALA2/Ethylene Response Factor (AP2/ERF) and Heat Shock Protein 90 (HSP90) are important classes of transcription factor and chaperone proteins known to play a significant role under stress. Productivity and yield of legume crops are severely affected by environmental and pathogen stresses. Genome sequences of chickpea, pigeonpea, common bean along with model legumes like medicago and lotus has aided in genome-wide identification of stress responsive AP2/ERF and HSP90 genes. HMM (Hidden Markov Model), blastp searches followed by domain scanning identified a total of 147 AP2/ERF genes in chickpea, 176 in pigeonpea, 179 in common bean, 131 in medicago and 140 in lotus. Sequences with one and two AP2 domains were classified as ERFs and AP2s respectively while sequences with AP2 and B3 domain were identified as RAVs. ERFs were further sub-classified into DREBs. Number of ERFs and DREBs ranged from 67 to 98 and 41 to 55 respectively in these crops. Two soloists were identified each in chickpea, pigeonpea and lotus; common bean with one and none in medicago. However, a very less number of HSP90 genes were identified in chickpea (5), pigeonpea (7), common bean (6), medicago (5) and lotus (5). Gene, protein structures, phylogenetic analyses, functional annotation and interaction networks provided basic insights in understanding the function of AP2/ERF and HSP90 genes. Expression studies using RNA-seq and qRT-PCR in response to heat and pathogen stress were also conducted in chickpea and pigeonpea respectively in search of probable candidate genes.

Inclusive Market-Oriented Development (IMOD) – our approach to bringing prosperity in the drylands. ICRISAT is a member of the CGIAR Consortium.

Abstract

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

*Address for correspondence: r.k.varshney@cgiar.org

Summary

A1 to E1: Phylogenetic relationships of AP2/ERF genes in chickpea, pigeonpea, common bean, medicago and lotus. In the unrooted trees, the ERFs are represented in green, DREBs in red, AP2s in blue; RAVs in pink. A2: Phylogenetic relationship of HSP 90 genes. A3: Expression profile of 22 AP2/ERF genes in vegetative, root, leaf and flower (before flowering) tissues is compared with reproductive, flower, root and leaf (after flowering) tissues of heat responsive chickpea genotypes.

A3

Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Pazhamala Lekha, Dadakhalandar Doddamani,

Aamir W Khan, Rajeev K Varshney *

Phylogenetic classification and expression analysis of AP2/ERF and HSP 90 genes A2

Genome-wide survey and characterization of AP2/ERF and HSP 90 gene family in five legume species

A4: Comparative analysis of orthologus relationship of

AP2/ERF and HSP 90 genes among five legumes.

A4: Expression profiles of 81 AP2/ERF genes based on log (base 2) of FPKM

values. Heat map (right) showing hierarchical clustering of AP2/ERF genes in

pigeonpea genotypes resistant and susceptible to Fusarium wilt (FW) and sterility

mosaic disease (SMD).

A3

A1: Representation of number of AP2, ERF, DREB,

RAV, soloist and HSP 90 genes.

A2 A3

A4

A1

A2

A4

A1-A3: Distribution of 179, 140, 140 AP2/ERF and 6, 5, 5 HSP 90 genes in phaseolus,

lotus and pigeonpea across chromosomes. Tandemly duplicated genes are

highlighted in color. Lines linking the genes represent segmentally duplicated genes.

Chromosomal distribution and expression analysis

A1 B1 C1

D1 E1

A1

A3

A2-A3: Distribution of AP2/ERF and HSP 90 genes

in chickpea and medicago. Tandemly duplicated

genes are highlighted in color. Lines linking the

genes represent segmentally duplicated genes.

A3

Chromosomal distribution and ortholog identification

Identified and characterized two important classes of transcription factor (AP2/ERF) and molecular chaperone

(HSP 90) proteins in the five select legumes

•Segmental duplication outnumbered tandem events with ERFs in most of the duplication events compared to DREBs

•HSP 90 proteins were clustered in two major groups based on their localization in the cell

•A total of 100, 80, 103 and 84 orthologs of chickpea AP2/ERF were identified in pigeonpea, medicago, common bean and lotus

• A total of 6 orthologs of chickpea HSP 90 were found in medicago, pigeonpea and common bean and 3 in lotus

chickpea & pigeonpea chickpea & lotus

chickpea & medicago chickpea & phaseolus

chickpea

&

four legumes

for HSP 90