Impact Factor 4.106 | CiteScore 4.47
More on impact ›

Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01570

Genetic Correlation, Genome-Wide Association and Genomic Prediction of Portable NIRS Predicted Carotenoids in Cassava Roots

  • 1Cornell University, United States
  • 2National Root Crops Research Institute, Nigeria
  • 3Robert W. Holley Center for Agriculture & Health, USDA-ARS, United States
  • 4International Institute of Tropical Agriculture (Nigeria), Nigeria

Random forests (RF) was used to correlate spectral responses to known wet chemistry carotenoid concentrations including total carotenoid content (TCC), all-trans β-carotene (ATBC), violaxanthin (VIO), lutein (LUT), 15-cis beta-carotene (15CBC), 13-cis beta-carotene (13CBC), alpha-carotene (AC), 9-cis beta-carotene (9CBC) and phytoene (PHY) from laboratory analysis of 173 cassava root samples in Columbia. The cross-validated correlations between the actual and estimated carotenoid values using RF ranged from 0.62 in PHY to 0.97 in ATBC. The developed models were used to evaluate the carotenoids of 594 cassava clones with spectral information collected across three locations in a national breeding program (NRCRI, Umudike), Nigeria. Both populations contained cassava clones characterized as white and yellow. The NRCRI evaluated phenotypes were used to assess the genetic correlations, conduct genome-wide association studies (GWAS) and genomic predictions. Estimates of genetic correlation showed various levels of the relationship among the carotenoids. The associations between TCC and the individual carotenoids were all significant (P < 0.001) with high positive values (r > 0.75, except in LUT and PHY where r < 0.3). The GWAS revealed significant genomic regions on chromosomes 1, 2, 4, 13, 14 and 15 associated with variation in at least one of the carotenoids. One of the identified candidate genes, phytoene synthase (PSY), has been widely reported for variation in TCC in cassava. On average, genomic prediction accuracies from the single-trait genomic best linear unbiased prediction (GBLUP) and RF as well as from a multiple-trait GBLUP model ranged from ~ 0.2 in LUT and PHY to 0.52 in TCC. The multiple-trait GBLUP model gave slightly higher accuracies than the single trait GBLUP and RF models. This study is one of the initial attempts in understanding the genetic basis of individual carotenoids and demonstrates the usefulness of NIRS in cassava improvement.

Keywords: Cassava (Manihot esculenta Crantz), Near Infra Red (NIR) spectroscopy, GWAS - genome-wide association study, Genomic prediction, Caroteinoids

Received: 27 May 2019; Accepted: 08 Nov 2019.

Copyright: © 2019 Ikeogu, Akdemir, Wolfe, Okeke, Amaefula, Jannink and Egesi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Ugochukwu N. Ikeogu, Cornell University, Ithaca, United States, uni3@cornell.edu