Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content

Adenike D Ige; Bunmi Olasanmi; Guillaume J Bauchet; Ismail S Kayondo; Edwige Gaby Nkouaya Mbanjo; Ruth Uwugiaren; Sharon Motomura-Wages; Joanna Norton; Chiedozie Egesi; Elizabeth Y Parkes; Peter Kulakow; Hernán Ceballos; Ibnou Dieng; Ismail Y Rabbi

doi:10.3389/fpls.2022.1016170

Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content

Front Plant Sci. 2022 Oct 12:13:1016170. doi: 10.3389/fpls.2022.1016170. eCollection 2022.

Authors

Adenike D Ige^{1

2}, Bunmi Olasanmi³, Guillaume J Bauchet⁴, Ismail S Kayondo¹, Edwige Gaby Nkouaya Mbanjo¹, Ruth Uwugiaren^{1

5}, Sharon Motomura-Wages⁶, Joanna Norton⁶, Chiedozie Egesi^{1

7}, Elizabeth Y Parkes¹, Peter Kulakow¹, Hernán Ceballos⁸, Ibnou Dieng¹, Ismail Y Rabbi¹

Affiliations

¹ International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria.
² Pan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, Nigeria.
³ Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan, Nigeria.
⁴ Boyce Thompson Institute, Ithaca, NY, United States.
⁵ Molecular Plant Sciences program, Washington State University, Pullman, WA, United States.
⁶ College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Hilo, HI, United States.
⁷ Cornell University, Ithaca, NY, United States.
⁸ The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia.

Abstract

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.

Keywords: allele-specific PCR; cassava (Manihot esculenta Crantz); dry matter content; marker-assisted selection; predictive accuracy; provitamin A content.