Structure of genetic diversity and genome-wide association studies of bean fly (Ophiomyia spencerella) resistance in common bean

Eastern Africa is a significant region of common bean (Phaseolus vulgaris L.) production and genetic diversity. Insect pests are a major biotic constraint in subsistence crop production systems. Bean fly (Ophiomyia spencerella) is a serious pest of beans in eastern Africa highlands. Breeding efforts focus on combining adaptability traits with user preferred seed types. However, lack of information on molecular markers linked to genes modulating bean fly resistance has slowed breeding progress. The objectives were to: (i) characterize genetic diversity and uncover putative bean fly resistant genotypes within diverse seed types and market classes and (ii) identify genomic regions controlling bean fly resistance using genome-wide association analysis (GWAS). A set of 276 diverse genotypes comprising local landraces and varieties from Kenya alongside introductions from International Centre for Tropical Agriculture (CIAT), were assembled. The germplasm represented varied bean production ecologies and seed types. Genetic diversity conforming to Andean and Mesoamerican genepools was established. Out of 276 genotypes evaluated, 150 were Andean, 74 were Mesoamerican and 52 were admixed. Twenty-two genotypes were resistant to bean fly. Association mapping results for stem damage score and plant mortality identified six significant single-nucleotide polymorphisms (SNPs) on chromosomes Pv01 and Pv09. The most significant SNP marker was 12 kilobases downstream of Phvul.001G074900 gene with LOD score > 4.0 hence in linkage disequilibrium with the postulated gene. The identified candidate gene is pleiotropic and modulates both flowering time and plant responses to stress. These findings are a key step towards marker-enabled breeding in common bean for sub-Saharan Africa.

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean

The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. This study’s objective was to determine the population structure of a diverse panel of common bean genotypes and deduce associations between bean fly resistance and agronomic traits based on single nucleotide polymorphism (SNP) markers. Ninety-nine common bean genotypes were phenotyped in two seasons at two locations and genotyped with 16 565 SNP markers. The genotypes exhibited significant variation for bean fly damage severity (BDS), plant mortality rate (PMR), and pupa count (PC). Likewise, the genotypes showed significant variation for agro-morphological traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield (GYD). The genotypes were delineated into two populations, which were based on the Andean and Mesoamerican gene pools. The genotypes exhibited a minimum membership coefficient of 0.60 to their respective populations. Eighty-three significant (P<0.01) markers were identified with an average linkage disequilibrium of 0.20 at 12Mb across the 11 chromosomes. Three markers were identified, each having pleiotropic effects on two traits: M100049197 (BDS and NPP), M3379537 (DTF and PC), and M13122571 (NPP and GYD). The identified markers are useful for marker-assisted selection in the breeding program to develop common bean genotypes with resistance to bean fly damage.

Genome-Wide Association Study of Resistance to Bean Fly and Population Structure of Market Classes of Common Bean

Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southern Africa region is widely driven by choice of grain types, which is affecting the genetic composition and adaptation to target production environments for biotic and abiotic constraints. Two bean fly species, Ophiomyia spencerella and Ophiomyia phaseoli are harmful insect pests of beans causing significant yield losses. Our objectives were to assess the population structure of common bean germplasm of different market classes and to identify polymorphic loci associated with resistance to O. spencerella. The study was carried out on a diversity panel of 284 genotypes using 9040 SNP markers. The genotypes were differentiated in to 14 distinct clusters. The mean FST of 0.4849, revealed major differentiation among the populations. Andean gene pool was more diverse compared to Mesoamerica gene pool which could be attributed to preference for large seeded cultivars. Multi-dimensional scaling and structure analyses revealed admixture among seed types. From genome wide association studies (GWAS), major genomic regions associated with O. spencerella resistance were identified on chromosome 1 (Pv01). The most significant SNP on Pv01 was aligned to gene PHAVU_001G075500g that is related to the Interleukin-1 receptor-associated kinase (IRAK) pathway, critical in regulating inherent immune responses to disease infection and insect herbivore attack. The diversity uncovered on the basis of market classes of beans and the presence of QTL regions associated with resistance to bean fly could serve as a valuable genetic resource for improvement of beans of different seed types in eastern and southern Africa region.

UJI TEKNIK PENGENDALIAN HAMA LALAT BIBIT (Ophiomyia phaseoli Try.) PADA TANAMAN KEDELAI (Glycine Max L.)

ABSTRAK Penelitian ini bertujuan untuk membandingkan teknik pengendalian yang lebih baik, guna mengurangi serangan hama Lalat Bibit Ophiomyia phaseoli Try. pada tanaman kedelai. Penelitian ini menggunakan metode eksperimental. Rancangan percobaan yang digunakan adalah Rancangan Acak Kelompok (RAK) dengan 4 perlakuan, setiap perlakuan diulang sebanyak 3 kali sehingga didapatkan 12 petak perlakuan. Perlakuan-perlakuan yang digunakan adalah K0 (Tanpa pelakuan), K1 (Penutup tanah), K2 (Seed treatment), K3 (Pupuk Hayati). Data hasil pengamatan dianalisis menggunakan analisis of variance (Anova) pada taraf 5%. Apabila siginificant (berbeda nyata) dilakukan uji lanjut menggunakan Uji Beda Nyata Jujur (BNJ) pada taraf 5%. Selanjutnya dilakukan regresi linier sederhana menggunakan Minitab 17. Hasil penelitian menunjukkan bahwa teknik pengendalian menggunakan seed treatment berpengaruh nyata terhadap populasi hama dan tingkat kerusakan tanaman. Populasi hama lalat bibit O. phaseoli Try. berpengaruh nyata terhadap tingkat kerusakan tanaman. ABSTRACT The aim of this study was to compare better control techniquesin order to reduce pest attacks of bean fly Ophiomyia phaseoli Try. on soybean plants. This study used an experimental method. The experimental design used was Randomized Complete Block Design (RCBD) with 4 treatments, each treatment was repeated 3 times, so that 12 treatment plots were obtained. The treatments used are K0 (without treatment), K1 (ground cover), K2 (seed treatment), K3 (biological fertilizer). Result of data observation were analyzed using analysis of variance (ANOVA) at the level of 5%. Honestly Significant Difference (HSD) Test at the level of 5% was carried out on significant results (significantly different). Furthermore, simple linear regression was performed using Minitab 17. The results of the study showed that the technical control using seed treatment had a significant effect on pest populations and plant attack rates. Population of bean fly O. phaseoli Try. were significantly affect the level of attack to plants.