Current advances in chickpea genomics: applications and future perspectives

Uday Jha

doi:10.1007/s00299-018-2305-6

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Publisher: Springer Journals
Copyright: Copyright © 2018 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject: Life Sciences; Plant Sciences; Cell Biology; Biotechnology; Plant Biochemistry
ISSN: 0721-7714
eISSN: 1432-203X
DOI: 10.1007/s00299-018-2305-6
pmid: 29860584
Publisher site: See Article on Publisher Site

Abstract

Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.

Journal

Plant Cell Reports – Springer Journals

Published: Jun 2, 2018

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Sharma, KD; Nayyar, H
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Sharma, R; Rawat, V; Suresh, CG
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Genetics and characterization of an open flower mutant in chickpea

Srinivasan, S; Gaur, PM
High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well asphasiRNA loci in chickpea

Srivastava, S; Zheng, Y; Kudapa, H; Jagadeeswaran, G; Hivrale, V; Varshney, RK; Sunkar, R
A high-resolution InDel (insertion–deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea

Srivastava, R; Singh, M; Bajaj, D; Parida, SK
Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

Srivastava, R; Bajaj, D; Sayal, YK; Meher, PK; Upadhyaya, HD; Kumar, R; Tripathi, S; Bharadwaj, C; Rao, AR; Parida, SK
Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

Srivastava, R; Bajaj, D; Malik, A; Singh, M; Parida, SK
A Multiple QTL-seq strategy delineates potential genomic loci governing flowering time in chickpea

Srivastava, R; Upadhyaya, HD; Kumar, R; Daware, A; Basu, U; Shimray, PW; Tripathi, S; Bharadwaj, C; Tyagi, AK; Parida, SK
QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

Takagi, H; Abe, A; Yoshida, K; Kosugi, S; Natsume, S; Mitsuoka, C; Uemura, A; Utsushi, H; Tamiru, M; Takuno, S; Innan, H; Cano, LM; Kamoun, S; Terauchi, R
Genetic mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.) using a simple sequence repeat linkage map

Tar’an, B; Warkentin, TD; Tullu, A; Vandenberg, A
Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches

Thudi, M; Upadhyaya, HD; Rathore, A; Gaur, PM; Krishnamurthy, L; Roorkiwal, M; Nayak, SN; Chaturvedi, SK; Basu, PS; Gangarao, NV; Fikre, A; Kimurto, P; Sharma, PC; Sheshashayee, MS; Tobita, S; Kashiwagi, J; Ito, O; Killian, A; Varshney, RK
Genomics-assisted breeding for drought tolerance in chickpea

Thudi, M; Gaur, PM; Krishnamurthy, L; Mir, RR; Kudapa, H; Fikre, A; Kimurto, P; Tripathi, S; Soren, KR; Mulwa, R; Bharadwaj, C; Datta, S; Chaturvedi, SK; Varshney, RK
Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum). BMC

Thudi, M; Khan, AW; Kumar, V; Gaur, PM; Katta, K; Garg, V; Roorkiwal, M; Samineni, S; Varshney, RK
Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

Thudi, M; Chitikineni, A; Liu, X; He, W; Roorkiwal, M; Yang, W; Jian, J; Doddamani, D; Gaur, PM; Rathore, A; Samineni, S; Saxena, RK; Xu, D; Singh, NP; Chaturvedi, SK; Zhang, G; Wang, J; Datta, SK; Xu, X; Varshney, RK
A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

Upadhyaya, HD; Bajaj, D; Das, S; Saxena, MS; Badoni, S; Kumar, V; Tripathi, S; Gowda, CL; Sharma, S; Tyagi, AK; Parida, SK
Genetic dissection of seed-iron and zinc concentrations in chickpea

Upadhyaya, HD; Bajaj, D; Das, S; Kumar, V; Gowda, CL; Sharma, S; Tyagi, AK; Parida, SK
Genome-wide scans for delineation of candidate genes regulating seed-protein content in chickpea

Upadhyaya, HD; Bajaj, D; Narnoliya, L; Das, S; Kumar, V; Gowda, CLL; Sharma, S; Tyagi, AK; Parida, SK
Genetic dissection of plant growth habit in chickpea

Upadhyaya, HD; Bajaj, D; Srivastava, R; Daware, A; Basu, U; Tripathi, S; Bharadwaj, C; Tyagi, AK; Parida, SK
Dynamics of colonization and expression of pathogenicity related genes in Fusarium oxysporum f.sp. ciceri during chickpea vascular wilt disease progression

Upasani, ML; Gurjar, GS; Kadoo, NY; Gupta, VS
Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

Upasani, ML; Limaye, BM; Gurjar, GS; Kasibhatla, SM; Joshi, RR; Kadoo, NY; Gupta, VS
Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor

Varma Penmetsa, R; Carrasquilla-Garcia, N; Bergmann, EM; Vance, L; Castro, B; Kassa, MT; Sarma, BK; Datta, S; Farmer, AD; Baek, JM; Coyne, CJ; Varshney, RK; Wettberg, EJ; Cook, DR
A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)

Varshney, RK; Hiremath, PJ; Lekha, P; Kashiwagi, J; Balaji, J; Deokar, AA; Vadez, V; Xiao, Y; Srinivasan, R; Gaur, PM; Siddique, KH; Town, CD; Hoisington, DA
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Varshney, RK; Song, C; Saxena, RK; Azam, S; Yu, S; Sharpe, AG; Cannon, S; Baek, J; Rosen, BD; Tar’an, B; Millan, T; Zhang, X; Ramsay, LD; Iwata, A; Wang, Y; Nelson, W; Farmer, AD; Gaur, PM; Soderlund, C; Penmetsa, RV; Xu, C; Bharti, AK; He, W; Winter, P; Zhao, S; Hane, JK; Carrasquilla-Garcia, N; Condie, JA; Upadhyaya, HD; Luo, MC; Thudi, M; Gowda, CL; Singh, NP; Lichtenzveig, J; Gali, KK; Rubio, J; Nadarajan, N; Dolezel, J; Bansal, KC; Xu, X; Edwards, D; Zhang, G; Kahl, G; Gil, J; Singh, KB; Datta, SK; Jackson, SA; Wang, J; Cook, DR
Fast-track introgression of ‘QTL-hotspot’ for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea

Varshney, RK; Gaur, PM; Chamarthi, SK; Krishnamurthy, L; Tripathi, S; Kashiwagi, J; Samineni, S; Singh, VK; Thudi, M; Jaganathan, D
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Varshney, RK; Mir, RR; Bhatia, S; Thudi, M; Hu, Y; Azam, S; Zhang, Y; Jaganathan, D; You, FM; Gao, J; Riera-Lizarazu, O; Luo, MC
Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.)

Varshney, RK; Thudi, M; Nayak, SN; Gaur, PM; Kashiwagi, J; Krishnamurthy, L; Jaganathan, D; Koppolu, J; Bohra, A; Tripathi, S; Rathore, A; Jukanti, AK; Jayalakshmi, V; Vemula, A; Singh, SJ; Yasin, M; Sheshshayee, MS; Viswanatha, KP
Marker-assisted backcrossing to introgress resistance to Fusarium wilt race 1 and Ascochyta blight in C214, an elite cultivar of chickpea

Varshney, RK; Mohan, SM; Gaur, PM; Chamarthi, SK; Singh, VK; Srinivasan, S; Swapna, N; Sharma, M; Singh, S; Kaur, L; Pande, S
High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using genotyping-by-sequencing (GBS)

Verma, S; Gupta, S; Bandhiwal, N; Kumar, T; Bharadwaj, C; Bhatia, S
CTDB: an integrated chickpea transcriptome database for functional and applied genomics

Verma, M; Kumar, V; Patel, RK; Garg, R; Jain, M
Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

Xu, X; Bai, G
Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.)

Yan, R; Liang, C; Meng, Z; Malik, W; Zhu, T; Zong, X; Guo, S; Zhang, R
Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

Yue, JX; Meyers, BC; Chen, JQ; Tian, D; Yang, S
Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

Zhou, Z; Jiang, Y; Wang, Z; Gou, Z; Lyu, J; Li, W; Yu, Y; Shu, L; Zhao, Y; Ma, Y; Fang, C; Shen, Y; Liu, T; Li, C; Li, Q; Wu, M; Wang, M; Wu, Y; Dong, Y; Wan, W; Wang, X; Ding, Z; Gao, Y; Xiang, H; Zhu, B; Lee, SH; Wang, W; Tian, Z

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Current advances in chickpea genomics: applications and future perspectives

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Current advances in chickpea genomics: applications and future perspectives

Current advances in chickpea genomics: applications and future perspectives

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