Mapping Quantitative Trait Loci (QTL) for Resistance to Bruchids (Callosobruchus maculatus) in Cowpea

Abstract

In storage, cowpea (Vigna unguiculata) experiences significant damage from biotic agents especially cowpea bruchids (Callosobruchus maculatus). This results in cowpea grain deterioration making the seeds unfit for human consumption as well as planting, hence posing a significant food security threat to humans and animals that depend on it as their source of food. Bruchid-resistant sources of cowpea genotypes have been identified in Uganda and elsewhere, however, these resistant sources are few, with low durability of resistance over time hence many studies have recommended continuous genetic improvement to maintain and increase their genetic base. Relatedly, the use of molecular marker tools and technologies has fastened the breeding process through marker-assisted selection/breeding made possible with the identification of new quantitative trait loci (QTL) or validation of already identified QTL for traits such as resistance to C. maculatus in cowpea. Therefore, the objectives of this study were to (1) Identify cowpea genotypes with high levels of resistance to bruchid (Callosobruchus maculatus) in cowpea bi-parental populations; and (2) to Identify Quantitative Trait Loci (QTL) associated with bruchid (Callosobruchus maculatus) resistance in the cowpea bi-parental population.

Bi-parental crosses were derived between susceptible and resistant cowpea parental genotypes; MU9 x WC42 and SECOW5T x 2419, respectively. The progenies derived out of the two crosses formed two independent populations. They were advanced up to F2 generation, and F2-derived F3 seeds were harvested for screening for resistance to C. maculatus. Leaf samples from each progeny at F2 were sampled at two weeks to extract DNA for genotyping using Diversity Arrays Technology (DArT) with 2753 sets of SNP markers. C. maculatus was used to infest the parents and progenies of each of the F2-derived F3 seeds from the two-cowpea bi-parental populations independently, under a no-choice experiment in a laboratory. This study was conducted at Makerere University Agricultural Research Institute Kabanyolo in Wakiso District between September 2021 and January 2022.

The results of the analysis of variance for evaluation of C. maculatus resistant traits showed significant differences (p≤ 0.05) among the cowpea progenies for the different seed weight and insect-derived parameters in both bi-parental populations. Relatedly, correlation analysis revealed that some of the bruchid-resistant traits are highly positively correlated, implying such traits can be selected together. Some progenies outperformed the resistant parent in each of the traits from the two bi-parental populations. Therefore, progenies Bi1-15, Bi1-130 and Bi1-110 from MU9 x WC42 cross; and Bi2-55, Bi2-149 and Bi2-46 from SECOW5T x 2419 cross had the lowest Dobie Susceptibility Index (DSI), and were the best progenies recommended for further evaluations for a possible release in future as varieties and as breeding lines for further improvement of C. maculatus resistance in other cowpea germplasms. The findings of this study showed that it is possible to obtain progenies with higher and better bruchid-resistance traits from bi-parental populations generated for bruchid resistance from the local sources, therefore suggesting the possibility of genetic improvement for this trait.

A linkage map of MU9 x WC42 derived mapping population was constructed with 582 polymorphic SNP markers that spanned a distance of 1504.81 cM, with an average distance of 2.60 cM between markers. Fourteen significant QTL signals were detected for both seed weight and insect-derived parameters using the composite interval mapping (CIM) method on seven of the eleven chromosomes of cowpea. QTL associated with seed weight traits mapped on chromosomes Vu03 and Vu09, whereas those associated with insect-derived parameters co-jointly mapped chromosomes Vu02, Vu03, Vu04, Vu06, Vu08 and Vu09 respectively. Three major QTL were identified including the number of adult bruchid emergence (NEI9.1MW), median development period (MDP6.1MW) and the average number of holes recorded (ANH9.1MW) on chromosomes Vu06 and Vu09 explaining 28.6%, 5.9% and 19.6% of the total phenotypic variations for the respective traits.

Additionally, QTL NE9.2MW for number of eggs laid linked to marker 2_16125 (A/C) at 43.0Mb, flanked by markers 2_16125 (43.0 Mb) and 2_13645 (42.2 Mb) on Vu09 is in the same genomic region with two previously reported QTL associated with number of eggs, percentage of damaged seeds, and developmental period near markers 2_38338 (T/A) (40.5 Mb) and SSR marker cp01354 (43.23 Mb) respectively. The markers linked to QTL identified in this study can be validated for marker-assisted selection to fasten breeding for resistance to C. maculatus traits in cowpea.