Development of a cost-effective high-throughput mid-density 5K genotyping assay for germplasm characterization and breeding in groundnut

被引：0

作者：

Pandey, Manish K. ^{[1
,2
]}

Sharma, Vinay ^{[1
,2
]}

Khan, Aamir W. ^{[1
,2
]}

Joshi, Pushpesh ^{[1
,2
]}

Gangurde, Sunil S. ^{[1
,2
]}

Bajaj, Prasad ^{[1
,2
]}

Janila, Pasupuleti ^{[1
,2
]}

Chitikineni, Annapurna ^{[1
,2
,8
]}

Bhat, Ramesh ^{[3
]}

Motagi, Babu N. ^{[3
]}

Sangh, Chandramohan ^{[4
]}

Radhakrishnan, Thankappan ^{[4
]}

Bera, Sandip K. ^{[4
]}

Gorjanc, Gregor ^{[5
,6
]}

Gujjula, Krishna Reddy ^{[7
]}

Hall, Nathan ^{[7
]}

Carrasco, Claudio D. ^{[7
]}

Arjun, Kandalam ^{[7
]}

Chandram, Srinivas ^{[7
]}

Varshney, Rajeev K. ^{[1
,2
,8
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, Ctr Excellence Genom & Syst Biol CEGSB, Hyderabad, India

[2] Int Crops Res Inst Semi Arid Trop, Ctr Prebreeding Res CPBR, Hyderabad, India

[3] Univ Agr Sci, Dept Biotechnol, Dharwad, India

[4] ICAR Indian Inst Groundnut Res IIGR, Junagadh, India

[5] Univ Edinburgh, Roslin Inst, Edinburgh, Scotland

[6] Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh, Scotland

[7] Thermo Fisher Sci, Waltham, MA USA

[8] Murdoch Univ, WA State Agr Biotechnol Ctr, Ctr Crop & Food Innovat, Murdoch, WA, Australia

来源：

PLANT GENOME | 2025年 / 18卷 / 02期

基金：

比尔及梅琳达.盖茨基金会;

关键词：

MARKER-ASSISTED SELECTION; ARACHIS-DURANENSIS; GENOME; INTROGRESSION; ASSOCIATION; RESISTANCE; OIL;

D O I：

10.1002/tpg2.70019

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Groundnut (Arachis hypogaea L.), also known as peanut, is an allotetraploid legume crop composed of two different progenitor sub-genomes. This crop is an important source for food, feed, and confectioneries. Leveraging translational genomics research has expedited the precision and speed in making selections of progenies in several crops through either marker-assisted selection or genomic selection, including groundnut. The availability of foundational genomic resources such as reference genomes for diploid progenitors and cultivated tetraploids, offered substantial opportunities for genomic interventions, including the development of genotyping assays. Here, a cost-effective and high-throughput genotyping assay has been developed with 5,081 single nucleotide polymorphisms (SNPs) referred to as "mid-density assay." This multi-purpose assay includes 5,000 highly informative SNPs selected based on higher polymorphism information content (PIC) from our previously developed high-density "Axiom_Arachis" array containing 58,233 SNPs. Additionally 82 SNPs associated with five resilience and quality traits were included for marker-assisted selection. To test the utility of the mid-density genotyping (MDG) assay, 2,573 genotypes from distinct sets of breeding populations were genotyped with the 5,081 SNPs. PIC of the SNPs in the MDG ranged from 0.34 to 0.37 among diverse sets. The first three principal components collectively explained 82.08% of the variance among these genotypes. The mid-density assay demonstrated a proficient ability to distinguish between the genotypes, offering a high level of genome-wide nucleotide diversity. This assay holds promise for possible deployment in the identification of varietal seed mixtures, genetic purity within gene bank germplasms and seed systems, foreground and background selection in backcross breeding programs, genomic selection, and sparse trait mapping studies in groundnut.

引用

页数：14

共 35 条

[1] Steady expression of high oleic acid in peanut bred by marker-assisted backcrossing for fatty acid desaturase mutant alleles and its effect on seed germination along with other seedling traits [J].

Bera, Sandip K. ;

Kamdar, Jignesh H. ;

Kasundra, Swati V. ;

Patel, Sahil V. ;

Jasani, Mital D. ;

Mauryal, A. K. ;

Dash, P. ;

Chandrashekar, Ajay B. ;

Rani, Kirti ;

Manivannan, N. ;

Janila, Pasupuleti ;

Pandey, Manish K. ;

Vasanthi, R. P. ;

Dobariya, K. L. ;

Radhakrishnan, T. ;

Varshney, Rajeev K. .

PLOS ONE, 2019, 14 (12)

[2] Improving oil quality by altering levels of fatty acids through marker-assisted selection of ahfad2 alleles in peanut (Arachis hypogaea L.) [J].

Bera, Sandip K. ;

Kamdar, Jignesh H. ;

Kasundra, Swati V. ;

Dash, Pitabas ;

Maurya, Anil K. ;

Jasani, Mital D. ;

Chandrashekar, Ajay B. ;

Manivannan, N. ;

Vasanthi, R. P. ;

Dobariya, K. L. ;

Pandey, Manish K. ;

Janila, Pasupuleti ;

Radhakrishnan, T. ;

Varshney, Rajeev K. .

EUPHYTICA, 2018, 214 (09)

[3] The genome sequence of segmental allotetraploid peanut Arachis hypogaea [J].

Bertioli, David J. ;

Jenkins, Jerry ;

Clevenger, Josh ;

Dudchenko, Olga ;

Gao, Dongying ;

Seijo, Guillermo ;

Leal-Bertioli, Soraya C. M. ;

Ren, Longhui ;

Farmer, Andrew D. ;

Pandey, Manish K. ;

Samoluk, Sergio S. ;

Abernathy, Brian ;

Agarwal, Gaurav ;

Ballen-Taborda, Carolina ;

Cameron, Connor ;

Campbell, Jacqueline ;

Chavarro, Carolina ;

Chitikineni, Annapurna ;

Chu, Ye ;

Dash, Sudhansu ;

El Baidouri, Moaine ;

Guo, Baozhu ;

Huang, Wei ;

Do Kim, Kyung ;

Korani, Walid ;

Lanciano, Sophie ;

Lui, Christopher G. ;

Mirouze, Marie ;

Moretzsohn, Marcio C. ;

Pham, Melanie ;

Shin, Jin Hee ;

Shirasawa, Kenta ;

Sinharoy, Senjuti ;

Sreedasyam, Avinash ;

Weeks, Nathan T. ;

Zhang, Xinyou ;

Zheng, Zheng ;

Sun, Ziqi ;

Froenicke, Lutz ;

Aiden, Erez L. ;

Michelmore, Richard ;

Varshney, Rajeev K. ;

Holbrook, C. Corley ;

Cannon, Ethalinda K. S. ;

Scheffler, Brian E. ;

Grimwood, Jane ;

Ozias-Akins, Peggy ;

Cannon, Steven B. ;

Jackson, Scott A. ;

Schmutz, Jeremy .

NATURE GENETICS, 2019, 51 (05) :877-+

[4] The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut [J].

Bertioli, David John ;

Cannon, Steven B. ;

Froenicke, Lutz ;

Huang, Guodong ;

Farmer, Andrew D. ;

Cannon, Ethalinda K. S. ;

Liu, Xin ;

Gao, Dongying ;

Clevenger, Josh ;

Dash, Sudhansu ;

Ren, Longhui ;

Moretzsohn, Marcio C. ;

Shirasawa, Kenta ;

Huang, Wei ;

Vidigal, Bruna ;

Abernathy, Brian ;

Chu, Ye ;

Niederhuth, Chad E. ;

Umale, Pooja ;

Araujo, Ana Claudia G. ;

Kozik, Alexander ;

Do Kim, Kyung ;

Burow, Mark D. ;

Varshney, Rajeev K. ;

Wang, Xingjun ;

Zhang, Xinyou ;

Barkley, Noelle ;

Guimaraes, Patricia M. ;

Isobe, Sachiko ;

Guo, Baozhu ;

Liao, Boshou ;

Stalker, H. Thomas ;

Schmitz, Robert J. ;

Scheffler, Brian E. ;

Leal-Bertioli, Soraya C. M. ;

Xun, Xu ;

Jackson, Scott A. ;

Michelmore, Richard ;

Ozias-Akins, Peggy .

NATURE GENETICS, 2016, 48 (04) :438-+

[5] Discovery of Major Quantitative Trait Loci and Candidate Genes for Fresh Seed Dormancy in Groundnut [J].

Bomireddy, Deekshitha ;

Gangurde, Sunil S. ;

Variath, Murali T. ;

Janila, Pasupuleti ;

Manohar, Surendra S. ;

Sharma, Vinay ;

Parmar, Sejal ;

Deshmukh, Dnyaneshwar ;

Reddisekhar, Mangala ;

Reddy, Devarapalli Mohan ;

Sudhakar, Palagiri ;

Reddy, Bommu Veera Bhaskara ;

Varshney, Rajeev K. ;

Guo, Baozhu ;

Pandey, Manish K. .

AGRONOMY-BASEL, 2022, 12 (02)

[6] 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

[7] Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.) [J].

Chen, Haodong ;

He, Hang ;

Zou, Yanjiao ;

Chen, Wei ;

Yu, Renbo ;

Liu, Xia ;

Yang, Yang ;

Gao, Yong-Ming ;

Xu, Jian-Long ;

Fan, Liu-Min ;

Li, Yi ;

Li, Zhi-Kang ;

Deng, Xing Wang .

THEORETICAL AND APPLIED GENETICS, 2011, 123 (06) :869-879

[8] Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement [J].

Chen, Xiaoping ;

Lu, Qing ;

Liu, Hao ;

Zhang, Jianan ;

Hong, Yanbin ;

Lan, Haofa ;

Li, Haifen ;

Wang, Jinpeng ;

Liu, Haiyan ;

Li, Shaoxiong ;

Pandey, Manish K. ;

Zhang, Zhikang ;

Zhou, Guiyuan ;

Yu, Jigao ;

Zhang, Guoqiang ;

Yuan, Jiaqing ;

Li, Xingyu ;

Wen, Shijie ;

Meng, Fanbo ;

Yu, Shanlin ;

Wang, Xiyin ;

Siddique, Kadambot H. M. ;

Liu, Zhong-Jian ;

Paterson, Andrew H. ;

Varshney, Rajeev K. ;

Liang, Xuanqiang .

MOLECULAR PLANT, 2019, 12 (07) :920-934

[9] Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens [J].

Chen, Xiaoping ;

Li, Hongjie ;

Pandey, Manish K. ;

Yang, Qingli ;

Wang, Xiyin ;

Garg, Vanika ;

Li, Haifen ;

Chi, Xiaoyuan ;

Doddamani, Dadakhalandar ;

Hong, Yanbin ;

Upadhyaya, Hari ;

Guo, Hui ;

Khan, Aamir W. ;

Zhu, Fanghe ;

Zhang, Xiaoyan ;

Pan, Lijuan ;

Pierce, Gary J. ;

Zhou, Guiyuan ;

Krishnamohan, Katta A. V. S. ;

Chen, Mingna ;

Zhong, Ni ;

Agarwal, Gaurav ;

Li, Shuanzhu ;

Chitikineni, Annapurna ;

Zhang, Guo-Qiang ;

Sharma, Shivali ;

Chen, Na ;

Liu, Haiyan ;

Janila, Pasupuleti ;

Li, Shaoxiong ;

Wang, Min ;

Wang, Tong ;

Sun, Jie ;

Li, Xingyu ;

Li, Chunyan ;

Wang, Mian ;

Yu, Lina ;

Wen, Shijie ;

Singh, Sube ;

Yang, Zhen ;

Zhao, Jinming ;

Zhang, Chushu ;

Yu, Yue ;

Bi, Jie ;

Zhang, Xiaojun ;

Liu, Zhong-Jian ;

Paterson, Andrew H. ;

Wang, Shuping ;

Liang, Xuanqiang ;

Varshney, Rajeev K. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (24) :6785-6790

[10] Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut [J].

Clevenger, Josh ;

Chu, Ye ;

Chavarro, Carolina ;

Agarwal, Gaurav ;

Bertioli, David J. ;

Leal-Bertioli, Soraya C. M. ;

Pandey, Manish K. ;

Vaughn, Justin ;

Abernathy, Brian ;

Barkley, Noelle A. ;

Hovav, Ran ;

Burow, Mark ;

Nayak, Spurthi N. ;

Chitikineni, Annapurna ;

Isleib, Thomas G. ;

Holbrook, C. Corley ;

Jackson, Scott A. ;

Varshney, Rajeev K. ;

Ozias-Akins, Peggy .

MOLECULAR PLANT, 2017, 10 (02) :309-322

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