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Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids

OAR@ICRISAT

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Relation http://oar.icrisat.org/10786/
http://dx.doi.org/10.1534/g3.118.200242
10.1534/g3.118.200242
 
Title Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids
 
Creator Liang, Z
Gupta, S K
Yeh, C T
Zhang, Y
Ngu, D W
Kumar, R
Patil, H T
Mungra, K D
Yadav, D V
Rathore, A
Srivastava, R K
Gupta, R
Yang, J
Varshney, R K
Schnable, P S
Schnable, J C
 
Subject Plant Breeding
Pearl Millet
Genetics and Genomics
 
Description Background: Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors' investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Results: Despite the fact that 6× more sequencing data were generated per sample for RAD-seq than for tGBS, tGBS yielded more than 2× as many informative SNPs (defined as those having MAF > 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000-grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (p
 
Publisher Genetics Society of America (GSA)
 
Date 2018-07
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/10786/1/Genome%20selection%20paper%20pearl%20millet%20ICRISAT.pdf
Liang, Z and Gupta, S K and Yeh, C T and Zhang, Y and Ngu, D W and Kumar, R and Patil, H T and Mungra, K D and Yadav, D V and Rathore, A and Srivastava, R K and Gupta, R and Yang, J and Varshney, R K and Schnable, P S and Schnable, J C (2018) Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids. G3: Genes, Genomes, Genetics (TSI), 8. pp. 2513-2522. ISSN 2160-1836