Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers.

Divya Sharma,Prabina Kumar Meher,N K Singh,Anil Kumar,Apoorv Tiwari,Gautam Jamra,Salej Sood,Manoj Prasad

doi:10.1371/journal.pone.0199444

Abstract

Finger millet (Eleusine coracana L.) is an important dry-land cereal in Asia and Africa because of its ability to provide assured harvest under extreme dry conditions and excellent nutritional properties. However, the genetic improvement of the crop is lacking in the absence of suitable genomic resources for reliable genotype-phenotype associations. Keeping this in view, a diverse global finger millet germplasm collection of 113 accessions was evaluated for 14 agro-morphological characters in two environments viz. ICAR-Vivekananda Institute of Hill Agriculture, Almora (E1) and Crop Research Centre (CRC), GBPUA&T, Pantnagar (E2), India. Principal component analysis and cluster analysis of phenotypic data separated the Indian and exotic accessions into two separate groups. Previously generated SNPs through genotyping by sequencing (GBS) were used for association mapping to identify reliable marker(s) linked to grain yield and its component traits. The marker trait associations were determined using single locus single trait (SLST), multi-locus mixed model (MLMM) and multi-trait mixed model (MTMM) approaches. SLST led to the identification of 20 marker-trait associations (MTAs) (p value<0.01 and <0.001) for 5 traits. While advanced models, MLMM and MTMM resulted in additional 36 and 53 MTAs, respectively. Nine MTAs were common out of total 109 associations in all the three mapping approaches (SLST, MLMM and MTMM). Among these nine SNPs, five SNP sequences showed homology to candidate genes of Oryza sativa (Rice) and Setaria italica (Foxtail millet), which play an important role in flowering, maturity and grain yield. In addition, 67 and 14 epistatic interactions were identified for 10 and 7 traits at E1 and E2 locations, respectively. Hence, the 109 novel SNPs associated with important agro-morphological traits, reported for the first time in this study could be precisely utilized in finger millet genetic improvement after validation.

Highlights

Finger millet [Eleusine coracana (L.) Gaertn] is a potential future crop because of its adaptability to environmental fluctuations and high nutritional value
The overall trend for all the observed traits was similar in both the locations. All these traits could be considered as good candidates for marker-trait associations (Table 2)
Our results indicate that epistatic interactions were important in the genetic control of grain yield and most of its component traits in finger millet

Summary

Introduction

Finger millet [Eleusine coracana (L.) Gaertn] is a potential future crop because of its adaptability to environmental fluctuations and high nutritional value. It is a self-pollinating allotetraploid (AABB) with basic chromosome number of 9 (2n = 4x = 36). The crop is thought to be domesticated in Uganda about 5000 years ago from where its cultivation extended to the Ethiopian highlands and India. The area occupied by the crop at the global level is estimated to be approximately 4.0–4.5 million hectares with a production of 5 million tonnes annually [1]. The high nutritive value of finger millet coupled with its ability to thrive under poor soil fertility and low rainfall conditions make it a climate-smart crop

Methods

Results

Discussion

Conclusion