MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)

Manchikatla, Praveen Kumar and Kalavikatte, Danamma and Mallikarjuna, Bingi Pujari and Palakurthi, Ramesh and Khan, Aamir W. and Jha, Uday Chand and Bajaj, Prasad and Singam, Prashant and Chitikineni, Annapurna and Varshney, Rajeev K. and Thudi, Mahandar (2021) MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.). Frontiers in Plant Science, 12:688694. pp. 1-11.

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MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.).pdf
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Abstract

Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Date Deposited: 18 Jan 2022 02:50
Last Modified: 19 Jan 2022 02:40
Uncontrolled Keywords: 100 seed weight; candidate genes and SNPs; chickpea; early flowering; MutMap
Fields of Research (2008): 07 Agricultural and Veterinary Sciences > 0703 Crop and Pasture Production > 070305 Crop and Pasture Improvement (Selection and Breeding)
Fields of Research (2020): 30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3004 Crop and pasture production > 300406 Crop and pasture improvement (incl. selection and breeding)
Socio-Economic Objectives (2008): B Economic Development > 82 Plant Production and Plant Primary Products > 8205 Winter Grains and Oilseeds > 820503 Grain Legumes
E Expanding Knowledge > 97 Expanding Knowledge > 970107 Expanding Knowledge in the Agricultural and Veterinary Sciences
Socio-Economic Objectives (2020): 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280101 Expanding knowledge in the agricultural, food and veterinary sciences
26 PLANT PRODUCTION AND PLANT PRIMARY PRODUCTS > 2603 Grains and seeds > 260303 Grain legumes
Identification Number or DOI: https://doi.org/10.3389/fpls.2021.688694
URI: http://eprints.usq.edu.au/id/eprint/45527

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