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Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing

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Title Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing
 
Creator Jaiswal, Vandana
Gupta, Sarika
Gahlaut, Vijay
Muthamilarasan, Mehanathan
Bandyopadhyay, Tirthankar
Ramchiary, Nirala
Prasad, Manoj
 
Subject Setaria italica
Foxtail Millet
ddRAD Sequencing
Major Agronomic Traits
 
Description Accepted date: 5 March 2019
Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
Te study was fnancially supported by Department of Biotechnology, Ministry of Science and Technology,
Government of India [BT/HRD/NBA/37/01/2014(vii)]. V.J., V.G. and M.M. acknowledge the DST-INSPIRE
Faculty Awards received from Department of Science and Technology, Ministry of Science and Technology,
Government of India. Te authors thank Dr. Swarup K Parida, Scientist, National Institute of Plant Genome
Research, New Delhi for his expert comments in improving the manuscript. Ms. Annvi Dhaka of National
Institute of Plant Genome Research, New Delhi is acknowledged for her assistance in the feld work. Te authors
are thankful to DBT-eLibrary Consortium (DeLCON) for providing access to e-resources.
 
Date 2019-03-28T05:43:20Z
2019-03-28T05:43:20Z
2019
 
Type Article
 
Identifier Scientific Reports 9(1): 5020
2045-2322
http://223.31.159.10:8080/jspui/handle/123456789/934
https://www.nature.com/articles/s41598-019-41602-6
https://doi.org/10.1038/s41598-019-41602-6
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature