Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea

被引：38

作者：

Saxena, Rachit K. ^{[1
]}

Kale, Sandip M. ^{[1
]}

Kumar, Vinay ^{[1
]}

Parupali, Swathi ^{[1
]}

Joshi, Shourabh ^{[2
]}

Singh, Vikas ^{[1
]}

Garg, Vanika ^{[1
]}

Das, Roma R. ^{[1
]}

Sharma, Mamta ^{[1
]}

Yamini, K. N. ^{[2
]}

Ghanta, Anuradha ^{[2
]}

Rathore, Abhishek ^{[1
]}

Sameerkumar, C. V. ^{[1
]}

Saxena, K. B. ^{[1
]}

Varshney, Rajeev K. ^{[1
,3
,4
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, Patancheru 502324, Andhra Prades, India

[2] PJTSAU, Inst Biotechnol, Hyderabad 500030, Andhra Prades, India

[3] Univ Western Australia, Sch Plant Biol, Crawley, WA 6009, Australia

[4] Univ Western Australia, Inst Agr, Crawley, WA 6009, Australia

来源：

SCIENTIFIC REPORTS | 2017年 / 7卷

关键词：

FUSARIUM-WILT; GENETIC-MAP; SOFTWARE; ELITE;

D O I：

10.1038/s41598-017-01535-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F-2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by- sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 x ICPL 332 (PRIL_B), ICPL 20097 x ICP 8863 (PRIL_C) and ICP 8863 x ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21cM), PRIL_C (484 SNPs; 798.25 cM) and F-2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

引用

页数：10

共 35 条

[1] Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers [J].

Baird, Nathan A. ;

Etter, Paul D. ;

Atwood, Tressa S. ;

Currey, Mark C. ;

Shiver, Anthony L. ;

Lewis, Zachary A. ;

Selker, Eric U. ;

Cresko, William A. ;

Johnson, Eric A. .

PLOS ONE, 2008, 3 (10)

[2] An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations [J].

Bohra, Abhishek ;

Saxena, Rachit K. ;

Gnanesh, B. N. ;

Saxena, Kulbhushan ;

Byregowda, M. ;

Rathore, Abhishek ;

KaviKishor, P. B. ;

Cook, Douglas R. ;

Varshney, Rajeev K. .

THEORETICAL AND APPLIED GENETICS, 2012, 125 (06) :1325-1338

[3] Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.) [J].

Bohra, Abhishek ;

Dubey, Anuja ;

Saxena, Rachit K. ;

Varma Penmetsa, R. ;

Poornima, K. N. ;

Kumar, Naresh ;

Farmer, Andrew D. ;

Srivani, Gudipati ;

Upadhyaya, Hari D. ;

Gothalwal, Ragini ;

Ramesh, S. ;

Singh, Dhiraj ;

Saxena, Kulbhushan ;

Kishor, P. B. Kavi ;

Singh, Nagendra K. ;

Town, Christopher D. ;

May, Gregory D. ;

Cook, Douglas R. ;

Varshney, Rajeev K. .

BMC PLANT BIOLOGY, 2011, 11

[4] TASSEL: software for association mapping of complex traits in diverse samples [J].

Bradbury, Peter J. ;

Zhang, Zhiwu ;

Kroon, Dallas E. ;

Casstevens, Terry M. ;

Ramdoss, Yogesh ;

Buckler, Edward S. .

BIOINFORMATICS, 2007, 23 (19) :2633-2635

[5]

CHURCHILL GA, 1994, GENETICS, V138, P963

[6] A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species [J].

Elshire, Robert J. ;

Glaubitz, Jeffrey C. ;

Sun, Qi ;

Poland, Jesse A. ;

Kawamoto, Ken ;

Buckler, Edward S. ;

Mitchell, Sharon E. .

PLOS ONE, 2011, 6 (05)

[7]

Ganapathy K. N., 2009, International Journal of Integrative Biology, V7, P145

[8] Development of genotyping by sequencing (GBS)- and array-derived SNP markers for stem rust resistance gene Sr42 [J].

Gao, Liangliang ;

Kielsmeier-Cook, Josh ;

Bajgain, Prabin ;

Zhang, Xiaofei ;

Chao, Shiaoman ;

Rouse, Matthew N. ;

Anderson, James A. .

MOLECULAR BREEDING, 2015, 35 (11)

[9] Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea [Cajanus cajan (L.) Millsp.] [J].

Gnanesh, B. N. ;

Bohra, A. ;

Sharma, M. ;

Byregowda, M. ;

Pande, S. ;

Wesley, V. ;

Saxena, R. K. ;

Saxena, K. B. ;

Kishor, P. B. Kavi ;

Varshney, R. K. .

FIELD CROPS RESEARCH, 2011, 123 (02) :53-61

[10] Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean [J].

Hart, John P. ;

Griffiths, Phillip D. .

PLANT GENOME, 2015, 8 (01)

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