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.).

Publication Overview
TitleMutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.).
AuthorsManchikatla PK, Kalavikatte D, Mallikarjuna BP, Palakurthi R, Khan AW, Jha UC, Bajaj P, Singam P, Chitikineni A, Varshney RK, Thudi M
TypeJournal Article
Journal NameFrontiers in plant science
Volume12
Year2021
Page(s)688694
CitationManchikatla PK, Kalavikatte D, Mallikarjuna BP, Palakurthi R, Khan AW, Jha UC, Bajaj P, Singam P, Chitikineni A, Varshney RK, Thudi M. 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. 2021; 12:688694.

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.

Features
This publication contains information about 12 features:
Feature NameUniquenameType
Ca6EF10099486Ca6EF10099486genetic_marker
Ca6EF10509893Ca6EF10509893genetic_marker
Ca6EF10670959Ca6EF10670959genetic_marker
Ca6EF10678606Ca6EF10678606genetic_marker
Ca6EF10685694Ca6EF10685694genetic_marker
Ca6EF9828083Ca6EF9828083genetic_marker
Ca6LF_10137361Ca6LF_10137361genetic_marker
Ca6LF_11657245Ca6LF_11657245genetic_marker
Ca6HSDW10190456Ca6HSDW10190456genetic_marker
Ca6HHSDW9828083Ca6HHSDW9828083genetic_marker
Ca6HSDW9890335Ca6HSDW9890335genetic_marker
Ca6LSDW9861219Ca6LSDW9861219genetic_marker
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-eCollection
ISSN1664-462X
pISSN1664-462X
Publication Date2021
Journal AbbreviationFront Plant Sci
DOI10.3389/fpls.2021.688694
Elocation10.3389/fpls.2021.688694
CopyrightCopyright © 2021 Manchikatla, Kalavikatte, Mallikarjuna, Palakurthi, Khan, Jha, Bajaj, Singam, Chitikineni, Varshney and Thudi.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountrySwitzerland
Cross References
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DatabaseAccession
PMID: PubMedPMID:34326857