Dataset Information

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

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.

SUBMITTER: Sharma D

PROVIDER: S-EPMC6084814 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Sharma Divya D Tiwari Apoorv A Sood Salej S Jamra Gautam G Singh N K NK Meher Prabina Kumar PK Kumar Anil A

PloS one 20180809 8

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 tw ...[more]

PMID: 30092057

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Project description:Finger millet, an orphan crop, possesses immense potential in mitigating climate change and could offer threefold security in terms of food, fodder, and nutrition. It is mostly cultivated as a subsistence crop in the marginal areas of plains and hills. Considering the changes in climate inclusive of recurrent weather vagaries witnessed every year, it is crucial to select stable, high-yielding, area-specific, finger millet cultivars. Sixty finger millet varieties released across the country were evaluated over six consecutive rainy seasons from 2011 to 2016 at the Agricultural Research Station, Vizianagaram. The genotype × environment interaction (GEI) was found to be significant in the combined ANOVA. Furthermore, the Additive Main effects and Multiplicative Interaction (AMMI) analysis asserted that genotypes and the GEI effects accounted for approximately 89% of the total variation. Strong positive associations were observed in an estimated set of eleven stability parameters which were chosen to identify stable genotypes. Furthermore, Non-parametric and Parametric Simultaneous Selection indices (NP-SSI and P-SSI) were calculated utilizing AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and Modified AMMI Stability Index (MASI) to identify stable high yielders. Both methods had inherent difficulties in ranking genotypes for SSI. To overcome this, the initial culling [i.e., SSI with culling strategy (C-SSI)] of genotypes was introduced for stability. In the C-SSI method, the top ten genotypes were above-average yielders, while those with below-average yield were observed in NP-SSI and P-SSI methods. Similarly, the estimation of best linear unbiased prediction (BLUP)-based simultaneous selections, such as harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), revealed that none of the top ten entries had below-average yield. The study has proven that C-SSI and BLUP-based methods were equally worthy in the selection of high-yielding genotypes with stable performance. However, the C-SSI approach could be the best method to ensure that genotypes with a considerable amount of stability are selected. The multi-year trial SSI revealed that entries Indaf-9, Sri Chaitanya, PR-202, and A-404; and VL324 and VL146 were ascertained to be the most stable high-yielding genotypes among medium-to-late and early maturity groups, respectively.

Dataset Information

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

Publications

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

Similar Datasets

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