Manchikatla, P K and Kalavikatte, D and Mallikarjuna, B P and Palakurthi, R and Khan, A W and Jha, U C and Bajaj, P and Singam, P and Chitikineni, A and Varshney, R K and Thudi, M (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 (TSI), 12. pp. 1-11. ISSN 1664-462X
![[img]](http://oar.icrisat.org/style/images/fileicons/application_pdf.png) |
PDF
- Published Version
Available under License ["licenses_description_cc_attribution" not defined]. Download (3MB) |
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.
| Item Type: | Article |
|---|---|
| Divisions: | Center of Excellence in Genomics and Systems Biology |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | MutMap, early flowering, chickpea, 100 seed weight, candidate genes and SNPs |
| Subjects: | Mandate crops > Chickpea Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 04 Jun 2025 08:15 |
| Last Modified: | 04 Jun 2025 08:15 |
| URI: | http://oar.icrisat.org/id/eprint/13116 |
| Official URL: | https://www.frontiersin.org/journals/plant-science... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | MT acknowledges financial support from the Science Engineering Research Board (SERB), Department of Science and Technology, Government of India (Grant ID: EEQ/2016/00348; Dated 20 February 2017). RKV is grateful to Bill and Melinda Gates Foundation for sponsoring the Tropical Legumes Project that partially supported this study (Grant ID: OPP1114827). This work has been carried out as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of the CGIAR System Organization. PKM is grateful to Council for Scientific and Industrial Research (CSIR), Ministry of Science and Technology, Government of India for awarding him fellowship during his Ph.D. research work. |
| Links: |
Actions (login required)
 |
View Item |
Altmetric
Altmetric