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Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

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Relation http://oar.icrisat.org/11679/
https://doi.org/10.3389/fnut.2020.559120
doi:10.3389/fnut.2020.559120
 
Title Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)
 
Creator Sab, S
Lokesha, R
Mannur, D M
Somasekhar, S
Jadhav, K
Mallikarjuna, B P
Laxuman, C
Yeri, S
Valluri, V
Bajaj, P
Chitikineni, A
Vemula, A K
Rathore, A
Varshney, R K
Shankergoud, I
Thudi, M
 
Subject Plant Nutrition
Chickpea
Genetics and Genomics
Food and Nutrition
Seeds/Seed Bank
 
Description Biofortification through plant breeding is a cost-effective and sustainable approach
towards addressing micronutrient malnutrition prevailing across the globe. Screening
cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes
and markers help in the development of biofortified varieties in chickpea (Cicer
arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and
Zn concentrations, the F2 : 3 population derived from a cross between MNK-1 and
Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated
for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839
single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with
an average marker density of 1.30 cM was constructed. By integrating the linkage
map data with the phenotypic data of the F2 : 3 population, a total of 11 QTLs were
detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic
variation explained ranging from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed Zn
concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The
QTLs individually explained phenotypic variations ranging between 5.7%(CaqZn8.1) and
13.7%(CaqZn4.3). Three QTLs for seed Fe and Zn concentrations (CaqFe4.4, CaqFe4.5,
and CaqZn4.1) were colocated in the “QTL-hotspot” region on CaLG04 that harbors
several drought tolerance-related QTLs. We identified genes in the QTL regions that
encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on
CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like
protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions
and the associated markers can be used in marker-assisted selection to increase seed
Fe and Zn concentrations in agronomically superior chickpea varieties.
 
Publisher Frontiers Media
 
Date 2020-10
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11679/1/fnut-07-559120.pdf
Sab, S and Lokesha, R and Mannur, D M and Somasekhar, S and Jadhav, K and Mallikarjuna, B P and Laxuman, C and Yeri, S and Valluri, V and Bajaj, P and Chitikineni, A and Vemula, A K and Rathore, A and Varshney, R K and Shankergoud, I and Thudi, M (2020) Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.). Frontiers in Nutrition (TSI), 7 (559120). pp. 1-9. ISSN 2296-861X