Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

被引：845

作者：

Varshney, Rajeev K. ^{[1
,2
]}

Song, Chi ^{[3
]}

Saxena, Rachit K. ^{[1
]}

Azam, Sarwar ^{[1
]}

Yu, Sheng ^{[3
]}

Sharpe, Andrew G. ^{[4
]}

Cannon, Steven ^{[5
]}

Baek, Jongmin ^{[6
]}

Rosen, Benjamin D. ^{[6
]}

Tar'an, Bunyamin ^{[7
]}

Millan, Teresa ^{[8
]}

Zhang, Xudong ^{[3
]}

Ramsay, Larissa D. ^{[4
]}

Iwata, Aiko ^{[9
]}

Wang, Ying ^{[3
]}

Nelson, William ^{[10
]}

Farmer, Andrew D. ^{[11
]}

Gaur, Pooran M. ^{[1
]}

Soderlund, Carol ^{[10
]}

Penmetsa, R. Varma ^{[6
]}

Xu, Chunyan ^{[3
]}

Bharti, Arvind K. ^{[11
]}

He, Weiming ^{[3
]}

Winter, Peter ^{[12
]}

Zhao, Shancen ^{[3
]}

Hane, James K. ^{[13
]}

Carrasquilla-Garcia, Noelia ^{[6
]}

Condie, Janet A. ^{[4
]}

Upadhyaya, Hari D. ^{[1
]}

Luo, Ming-Cheng ^{[6
]}

Thudi, Mahendar ^{[1
]}

Gowda, C. L. L. ^{[1
]}

Singh, Narendra P. ^{[14
]}

Lichtenzveig, Judith ^{[15
]}

Gali, Krishna K. ^{[4
]}

Rubio, Josefa ^{[8
]}

Nadarajan, N. ^{[16
]}

Dolezel, Jaroslav ^{[17
]}

Bansal, Kailash C. ^{[18
]}

Xu, Xun

Edwards, David ^{[19
,20
]}

Zhang, Gengyun ^{[3
]}

Kahl, Guenter ^{[21
]}

Gil, Juan ^{[8
]}

Singh, Karam B. ^{[13
,22
]}

Datta, Swapan K. ^{[23
]}

Jackson, Scott A. ^{[9
]}

Wang, Jun ^{[3
,24
]}

Cook, Douglas R. ^{[6
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, Hyderabad, Andhra Pradesh, India

[2] CGIAR Generat Challenge Programme, Texcoco, Mexico

[3] Beijing Genom Inst BGI Shenzhen, Shenzhen, Peoples R China

[4] Natl Res Council Canada NRC CNRC, Ottawa, ON, Canada

[5] Iowa State Univ, USDA ARS, Ames, IA USA

[6] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA

[7] Univ Saskatchewan, Ctr Crop Dev, Saskatoon, SK S7N 0W0, Canada

[8] Univ Cordoba, Dept Genet, Cordoba, Spain

[9] Univ Georgia, Ctr Appl Genet Technol, Athens, GA 30602 USA

[10] Univ Arizona, Tucson, AZ USA

[11] NCGR, Santa Fe, NM USA

[12] GenXPro GmbH, Frankfurt, Germany

[13] CSIRO, Canberra, ACT, Australia

[14] ICAR Res Complex, All India Coordinated Res Project Chickpea AICRP, New Delhi, India

[15] Curtin Univ, Bentley, WA, Australia

[16] ICAR Res Complex, IIPR, Kanpur, Uttar Pradesh, India

[17] Inst Expt Bot, Ctr Reg Hana Biotechnol & Agr Res, Olomouc, Czech Republic

[18] ICAR Res Complex, NBPGR, New Delhi, India

[19] ACPFG, St Lucia, Qld, Australia

[20] Univ Queensland, St Lucia, Qld, Australia

[21] Goethe Univ Frankfurt, D-60054 Frankfurt, Germany

[22] Univ Western Australia, Univ Western Australia Inst Agr, Crawley, Australia

[23] ICAR Res Complex, Div Crop Sci, New Delhi, India

[24] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

来源：

NATURE BIOTECHNOLOGY | 2013年 / 31卷 / 03期

基金：

美国国家科学基金会; 澳大利亚研究理事会; 美国食品与农业研究所;

关键词：

L; INTEGRATION; EVOLUTION; QUALITY; LEGUME;

D O I：

10.1038/nbt.2491

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the similar to 738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea-desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

引用

页码：240 / 246

页数：7

共 19 条

[1] A draft genome sequence of the pulse crop chickpea (Cicer arietinumL.)
Jain, Mukesh
Misra, Gopal
Patel, Ravi K.
Priya, Pushp
Jhanwar, Shalu
Khan, Aamir W.
Shah, Niraj
Singh, Vikas K.
Garg, Rohini
Jeena, Ganga
Yadav, Manju
Kant, Chandra
Sharma, Priyanka
Yadav, Gitanjali
Bhatia, Sabhyata
Tyagi, Akhilesh K.
Chattopadhyay, Debasis
PLANT JOURNAL, 2013, 74 (05) : 715 - 729
[2] An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
Parween, Sabiha
Nawaz, Kashif
Roy, Riti
Pole, Anil K.
Suresh, B. Venkata
Misra, Gopal
Jain, Mukesh
Yadav, Gitanjali
Parida, Swarup K.
Tyagi, Akhilesh K.
Bhatia, Sabhyata
Chattopadhyay, Debasis
SCIENTIFIC REPORTS, 2015, 5
[3] Assembling a puzzle of dispersed retrotransposable sequences in the genome of chickpea (Cicer arietinum L.)
Staginnus, C.
Desel, C.
Schmidt, T.
Kahl, G.
GENOME, 2010, 53 (12) : 1090 - 1102
[4] Genome-wide association study in Chickpea (Cicer arietinum L.) for yield and nutritional components
Sari, Hatice
Uhdre, Renan
Wallace, Lyle
Coyne, Clarice J.
Bourland, Britton
Zhang, Zhiwu
Russo, M.
Kiszonas, Alecia
Warburton, Marilyn L.
EUPHYTICA, 2024, 220 (06)
[5] Identification of Sclerotinia stem rot resistance quantitative trait loci in a chickpea (Cicer arietinum) recombinant inbred line population
Mwape, Virginia W.
Khoo, Kelvin H. P.
Chen, Kefei
Khentry, Yuphin
Newman, Toby E.
Derbyshire, Mark C.
Mather, Diane E.
Kamphuis, Lars G.
FUNCTIONAL PLANT BIOLOGY, 2022, 49 (07) : 634 - 646
[6] Genome-wide identification and structure-function studies of proteases and protease inhibitors in Cicer arietinum (chickpea)
Sharma, Ranu
Suresh, C. G.
COMPUTERS IN BIOLOGY AND MEDICINE, 2015, 56 : 67 - 81
[7] Genetic Variability in Food and Feed Traits of Early Maturing Desi Chickpea (Cicer arietinum) for Multi-Dimensional Improvement
Alkhtib, A.
Wamatu, J.
Ejeta, T. T.
Rischkowsky, B.
ANIMAL NUTRITION AND FEED TECHNOLOGY, 2018, 18 (03) : 389 - 398
[8] Demystifying the nutritional and anti-nutritional genetic divergence of Pakistani chickpea (Cicer arietinum L.) genetic resource via multivariate approaches
Jameel, Saima
Hameed, Amjad
Shah, Tariq Mahmud
Coyne, Clarice J.
FRONTIERS IN NUTRITION, 2024, 11
[9] Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)
Pradhan, Seema
Kant, Chandra
Verma, Subodh
Bhatia, Sabhyata
PLOS ONE, 2017, 12 (07):
[10] STMS (sequence tagged microsatellite site) molecular markers as a valuable tool to confirm controlled crosses in chickpea (Cicer arietinum L.) breeding programs
C. Caballo
P. Castro
J. Gil
I. Izquierdo
T. Millan
J. Rubio
Euphytica, 2018, 214

← 1 2 →