|dc.description.abstract||The common bean (Phaseolus vulgaris L.) is the second most important food legume in Ethiopia. It is the most important cash crop for the smallholder farmers and has a significant impact on the national economy. However, the productivity of the crop is hampered by many biotic and abiotic stress factors. In recent years, the Mexican bean weevil (Zabrotes subfasciatus Boheman), hereafter also called bruchid, has been causing significant grain losses in storage. Therefore, the objectives of the present study are as follows: (a) to evaluate the Ethiopian common bean landrace collections, commercial varieties, advanced breeding lines and elite resistant lines for resistance to the Mexican bean weevil; (b) to assess the magnitude and pattern of genetic diversity in Ethiopian common bean landraces, commercial varieties, advance breeding and exotic resistant lines for the response to infestation by bean bruchid, using phenotypic and SNP markers; (c) to examine the population structure among common bean genotypes collected from different breeding status, seed colours and sizes, and to identify genomic regions that are associated with bean bruchid resistance, using SNP markers distributed across common bean genome; (d) to assess the agronomic performance of common bean genotypes selected for their response to bruchid infestation, using yield and yield components under different agro-ecologies; (e) to identify suitable parental genotypes that are useful for breeding for bruchid resistance and to identify the farmers’ selection criteria for choosing varieties; and (f) to interogress arcelin genes into commercial varieties and an advanced breeding line. For this study, a total of 300 common bean genotypes were phenotyped for bruchid resistance under laboratory conditions, and they were genotyped, using Illumina BARCBean6K_3 SNP BeadChip. Data on insect and seed traits were used for genetic diversity and genome-wide marker-trait association analysis. One-hundred and-forty-four genotypes were selected, based on their level of resistance, population structure and genetic distances and they were evaluated under three different agro-ecological field conditions, for yield and yield-related traits. Participatory variety selection (PVS) was also conducted for the selected genotypes. Subsequently, six female parents and seven donner lines were selected, based on the farmers’ traits of interest, level of resistance and suitable agronomic traits, of which one commercial variety and one advanced breeding line were crossed with one donor Marker Assisted Zabrotes (MAZ) resistant lines. The segregating population was phenotyped for bruchid resistance at the F4 generation.
The laboratory screening of the genotypes revealed that a wide range of variation was recorded among the landraces, commercial varieties, advanced breeding and resistant lines for all the parameters studied. Absolute resistance was recorded only from the resistant lines, namely RAZ-11, RAZ-36, RAZ-2, RAZ-44, RAZ-120, RAZ-40, MAZ-200 and MAZ-203, while the majority of the local germplasm was found to be susceptible. Some of the local germplasm showed a partial resistance to bean bruchid and two promising entries were identified, namely, SCR-11 (breeding line) and NC-16 (landrace).
The genetic diversity analysis, using phenotypic and SNP markers, revealed that considerable variation was existed among the Ethiopian common bean genotypes. High phenotypic diversity indices among phenotypic traits were recorded. The principal component analyses identified four PCs that explained 82% of the total phenotypic variation among genotypes. The polymorphic information content (PIC) ranged from 0.21 to 0.38, with a mean 0.34, reflecting the relatively high discriminating ability of the SNP markers. More than 70% of the gene diversity was recorded within the common bean population that were classified according to their breeding status and seed size. The four and two populations that were based on breeding status and seed size, respectively, were highly differentiated. Both the SNP and the phenotypic markers grouped the 297 common bean genotypes into two major distinct clusters and three sub-clusters, irrespective of their geographic origin.
The population structure analysis, based on Bayesian genotyping clustering approach, classified the common bean genotypes into two populations, namely, the Middle American and Andean gene pools. Similar population patterns were also observed by using the principal coordinate analysis (PCoA). The genome-wide association study (GWAS) identified 24 single-nucleotide polymorphism (SNP) markers on nine chromosomes, with a significant (P < 0.05) association with a percentage adult emergence (PAE) and a percentage seed weight loss (PSWL). However, only 13 SNPs located on Chromosomes 4 and 7 were significantly (P < 0.001) associated with the two traits. Other significant SNPs were identified on other chromosomes of the common bean, but none of them were above the cutoff point (1.00 × 10−4).
Based on the above analyses, 144 diverse genotypes were selected and evaluated at three sites. Six principal components (PCs) were identified that explained 84% of the total variation among the genotypes. The 15 agro-morphological traits classified the genotypes into three distinct major clusters and sub-clusters. The clustering patterns of the genotypes were according to the seed size, in which small and medium beans were distinctly separated from the large seeded beans. The study established the existence of considerable genetic variation among common bean genotypes. Unique genotypes, such as Nasir, Awash Melka and RAZ-36 from Cluster I, RAZ-2, RAZ-11 and RAZ-42 from Cluster II and SER-125, SCR-15, MAZ-200, MAZ-203 and RAZ-120 from Cluster III were selected, based on their distinct agronomic performance and their response to the Mexican bean weevil infestation. The participatory variety selection revealed that farmers used complex and diverse selection criteria in different agro-ecologies. The selection criteria varied among agro-ecologies and gender groups. Yield and yield-related traits were ranked as the most important selection criteria in all the locations and gender groups. Women ranked the taste and cooking time as the top criteria for varietal choice, while men were more interested in marketability, seed size and colour. In all three agro-ecologies, both farmer groups were able to select the top 10 best genotypes, although varietal preferences across locations and gender groups were diverse. The top set of selected genotypes matched the breeders’ selection, with only minor difference.
The phenotyping of the F4 families derived from SCR-15 X MAZ-200 crosses showed highly significant differences (P < 0.001) among the entries, parents and offspring for all of the susceptible parameters, except the number of eggs. Based on the percentage adult emergence, 34.6% of the progeny genotypes were categorized as highly resistant, 12.0% were resistant, 21.6% were moderately resistant and 32.7% were susceptible. The study observed considerable phenotypic variation among the offspring and parental lines for the susceptibility parameters. The levels of broad sense heritability ranged from 68.5% – 93.9% for all the traits, suggesting that selection may be useful to improve bruchid resistance. In general, the study has identified absolute resistant lines among the exotic germplasm, while partial resistance genotypes among the Ethiopian genotypes signifies the possibility of the introgression of the resistance genes. The information reported in this study could serve as an important benchmark for future common bean breeding and conservation programs.||en_US