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Current advances in chickpea genomics: applications and future perspectives

Current advances in chickpea genomics: applications and future perspectives 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Cell Reports Springer Journals

Current advances in chickpea genomics: applications and future perspectives

Jha, Uday
Plant Cell Reports , Volume 37 (7) – Jun 2, 2018
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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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  • An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
    Parween, S; Nawaz, K; Roy, R; Pole, AK; Venkata Suresh, B; Misra, G; Jain, M; Yadav, G; Parida, SK; Tyagi, AK; Bhatia, S; Chattopadhyay, D
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  • Global transcriptome analysis of developing chickpea (Cicerarietinum L.) seeds
    Pradhan, S; Bandhiwal, N; Shah, N; Kant, C; Gaur, R; Bhatia, S
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    Purayannur, S; Kumar, K; Kaladhar, VC; Verma, PK
  • Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines
    Pushpavalli, R; Krishnamurthy, L; Thudi, M; Gaur, PM; Rao, MV; Siddique, KH; Colmer, TD; Turner, NC; Varshney, RK; Vadez, V
  • DNA methylation and physio-biochemical analysis of chickpea in response to cold stress
    Rakei, A; Maali-Amiri, R; Zeinali, H; Ranjbar, M
  • Identification and expression analysis of candidate genes involved in carotenoid biosynthesis in chickpea seeds
    Rezaei, MK; Deokar, A; Tar’an, B
  • Marker-assisted selection to improve drought adaptation in maize: the backcross approach, perspectives, limitations, and alternatives
    Ribaut, JM; Ragot, M
  • The chickpea early flowering 1 (Efl1) locus is an ortholog of arabidopsis ELF3
    Ridge, S; Deokar, A; Lee, R; Daba, K; Macknight, RC; Weller, JL; Tar’an, B
  • Genome-enabled prediction models for yield related traits in chickpea
    Roorkiwal, M; Rathore, A; Das, RR; Singh, MK; Jain, A; Srinivasan, S; Gaur, PM; Chellapilla, B; Tripathi, S; Li, Y; Hickey, JM; Lorenz, A; Sutton, T; Crossa, J; Jannink, JL; Varshney, RK
  • Study on chickpea drought tolerance lines under dryland condition of Iran
    Sabaghpour, SH; Mahmodi, AA; Kamel, SM; Malhotra, RS
  • Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)
    Sabbavarapu, MM; Sharma, M; Chamarthi, SK; Swapna, N; Rathore, A; Thudi, M; Gaur, PM; Suresh Pande, S; Singh, S; Kaur, L; Varshney, RK
  • Genetic analysis of NBS-LRR gene family in chickpea and their expression profiles in response to ascochyta blight infection
    Sagi, MS; Deokar, AA; Tar’an, B
  • Differentially expressed myo-inositol monophosphatase gene (CaIMP) in chickpea (Cicer arietinum L.) encodes a lithium-sensitive phosphatase enzyme with broad substrate specificity and improves seed germination and seedling growth under abiotic stresses
    Saxena, SC; Salvi, P; Kaur, H; Verma, P; Petla, BP; Rao, V; Kamble, N; Majee, M
  • An integrated genomic approach for rapid delineation of candidate genes regulating agro-morphological traits in chickpea
    Saxena, MS; Bajaj, D; Das, S; Kujur, A; Kumar, V; Singh, M; Bansal, KC; Tyagi, AK; Parida, SK
  • Targeted genome modification of crop plants using a CRISPR-Cas system
    Shan, Q; Wang, Y; Li, J; Zhang, Y; Chen, K; Liang, Z; Zhang, K; Liu, J; Xi, JJ; Qiu, JL; Gao, C
  • Cold stress alters transcription in meiotic anthers of cold tolerant chickpea (Cicer arietinum L.)
    Sharma, KD; Nayyar, H
  • Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome
    Sharma, R; Rawat, V; Suresh, CG
  • Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)
    Sharma, R; Rawat, V; Suresh, CG
  • Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
    Singh, VK; Jain, M
  • A global view of transcriptome dynamics during flower development in chickpea by deep sequencing
    Singh, VK; Garg, R; Jain, M
  • QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea
    Singh, VK; Khan, AW; Jaganathan, D; Thudi, M; Roorkiwal, M; Takagi, H; Garg, V; Kumar, V; Chitikineni, A; Gaur, PM; Sutton, T; Terauchi, R; Varshney, RK
  • PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea
    Singh, U; Khemka, N; Rajkumar, MS; Garg, R; Jain, M
  • Genome-wide identification of the MAPK gene family in chickpea and expression analysis during development and stress response
    Singh, A; Nath, O; Singh, S; Kumar, S; Singh, IK
  • Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome
    Sivasakthi, K; Thudi, M; Tharanya, M; Kale, SM; Kholová, J; Halime, MH; Jaganathan, D; Baddam, R; Thirunalasundari, T; Gaur, PM; Varshney, RK; Vadez, V
  • 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