Validation of sorghum quality control (QC) markers across African breeding lines

Gimode, D M and Ochieng, G and Deshpande, S P and Manyasa, E O and Kondombo, C P and Mikwa, E O and Avosa, M O and Kunguni, J S and Ngugi, K and Sheunda, P and Jumbo, M B and Odeny, D A (2024) Validation of sorghum quality control (QC) markers across African breeding lines. The Plant Genome (TSI). pp. 1-11. ISSN 1940-3372

PDF - Published Version Available under License ["licenses_description_cc_attribution" not defined]. Download (1MB)

Abstract

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.

Item Type:	Article
Divisions:	Global Research Program - Accelerated Crop Improvement Research Program : East & Southern Africa Research Program : West & Central Africa
CRP:	UNSPECIFIED
Uncontrolled Keywords:	quality control (QC) markers, sorghum, African breeding lines, single nucleotide polymorphism (SNP) markers
Subjects:	Mandate crops > Sorghum Others > Genetics and Genomics Others > Africa
Depositing User:	Mr Nagaraju T
Date Deposited:	14 Jun 2024 10:50
Last Modified:	14 Jun 2024 10:50
URI:	http://oar.icrisat.org/id/eprint/12708
Official URL:	https://acsess.onlinelibrary.wiley.com/doi/full/10...
Projects:	UNSPECIFIED
Funders:	CGIAR Research Program (CRP)
Acknowledgement:	This work was partially funded by the CGIAR Research Program (CRP) on Grain Legumes and Dryland Cereals, the Excellence in Breeding Platform and the Bill and Melinda Gates Foundation. The authors acknowledge the coordination of genotyping services by the Excellence in Breeding Platform staff, especially Milcah Kigoni, Ana Oliveira, and Ng Eng Hwa.
Links:	Google Scholar

View Statistics

Actions (login required)

View Item