Abstract
Seed traits of bread wheat, including the seed size that is considered to be associated with early vigor of the crop and end-use quality, are valuable to farmers and breeders. In this study, a collection of 789 bread wheat landraces, held in-trust at the genebank of the International Center for Agricultural Research in the Dry Areas (ICARDA) were scanned for seed morphometric traits using GrainScan. Diversity analysis using the 12k DartSeq SNP markers revealed that these accessions can be grouped into five distinct clusters. To evaluate the performance for early selection from genebank accessions, we examined the accuracy of genomic selection models with genomic relationship that these landraces accounted for. Based on cross-validations, prediction accuracies for seed traits ranged from 0.64 for seed perimeter to 0.74 for seed width. The variability of prediction accuracies across random validations averaged at 0.14, with a range from 0.12 to 0.18, suggesting stable predictability and reproducible results even with a collection of much greater genetic diversity from genebank accessions. Adding the climatic relationship matrix between accessions based on passport information improved the predictive ability by 8%. Our results on seed traits demonstrated the capacity for estimating important agronomic phenotypes for genebank accessions directly based on genomic information, further advocating the advance in genomic technologies for identifying parental germplasm as potential donors of beneficial alleles for introgression.
Highlights
Wheat is one of the most important cultivated food crops, and its cultivation goes back some 11,000–10,000 years ago (Nesbitt, 2002; Zohary et al, 2012)
To evaluate the impact of population structure in the performance of genomic prediction, we evaluated the following models: (1) null model where no population structure was accounted for; (2) accounting for population structure using discrete population resulting from discriminate analysis of principal component (DAPC) with K number of subpopulations equal to 2 which is the first level of genetic separation; (3) accounting for population structure using discrete population resulting from DAPC with K optimal number of subpopulations; (4) accounting for population structure using 5 eigen vectors PC1 to PC5 resulting from principal component analysis (PCA) analysis
The set of landraces used in this study exhibited population structure as shown by plotting first versus second principal component (Figure 1)
Summary
Wheat is one of the most important cultivated food crops, and its cultivation goes back some 11,000–10,000 years ago (Nesbitt, 2002; Zohary et al, 2012). Wheat has been the fundamental staple food for the majority of human civilizations in Europe, West Asia, and North Africa (Curtis et al, 2002) because of its crucial nutritional value and its significant contribution to daily energy intake. To secure an efficient continuum between the conservation and the use of genetic resources, wheat accessions need to be well-characterized and evaluated for a range of traits. The study of this phenotypic diversity will result in better use in breeding programs
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
