Combining ability and genetic mappig of pod quality and yield traits in locally adapted french beans (phaseolus vulgaris l.) in Kenya

Abstract

French beans are common beans (Phaseolus vulgaris L.) that have palatable pods. The crop is mostly grown for export, supporting Kenyan smallholder farmers. In Eastern Africa, developing French bean varieties with high pod yield, good pod quality, and processing industry has received little research, and there is limited information on genetics of pod quality and yield traits. This study investigated the genetics underlying French bean pod quality and yield, with crucial characteristics for the development of improved varieties in Kenya. The first objective focus was on evaluation of commercial French bean varieties for pod quality and yield performance. Thirteen French bean and two dry bean varieties were tested for pod quality and yield in Embu and Mwea, to select material for further research. Later, a half-diallel population was developed from five French bean and two dry bean varieties. The aim was to examine the gene action of French bean pod attributes and to identify parents with good combining abilities. Additionally, a cross between French bean × dry bean, was used to develop a population of recombinant inbred lines (RILs) specifically using the Vanilla × MCM5001 varieties, to facilitate genetic mapping of traits associated with French bean pod quality and yield. Data on various pod traits of the RILs and parents were collected from plants that were planted in three trials in Kenya and the University of California, Davis greenhouse. In addition, genomic DNA from the RILs and parents were genotyped using single nucleotide polymorphisms (SNPs). Results from diallel analysis revealed significant (P < 0.001) general and specific combining abilities effects for the evaluated traits. This highlighted the significance of additive and dominance gene effects, with the predominance of additive gene effects. The crosses between Serengeti × Amy, Serengeti × Moonstone, and Serengeti × G2333 were best combiners for pod quality, whereas G2333 × Amy and Moonstone × Amy produced best progenies for pod yield. Using SNPs and phenotypic data from 184 F2:6 RILs, 44 quantitative trait loci (QTL) were discovered for yield and pod quality traits through QTL mapping. The QTL for pod yield were identified on chromosomes Pv03 and Pv08, while the QTL for pod quality were located on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07. In addition, six novel QTL were identified, whereas others overlapped with pod quality and yield QTL. Using the mapping results, candidate genes responsible for French bean pod string (St) were identified and eight gel-based molecular markers were developed and tested for their suitability for marker-assisted selection (MAS). The results indicated that six of the eight markers amplified DNA from Vanilla and MCM 5001, although only one marker revealed variation between the parents and RILs. Chi-square analysis identified a significant (P < 0001) association between the pod string score and the marker, linked at 7.8 cM from St. The identified QTL and markers can facilitate development of more robust molecular markers and for further studies on French bean pod quality and yield. In addition, varieties with the best combining abilities (Serengeti × Moonstone, MCM 5001 × Amy and Vanilla × Moonstone) can serve as parents in breeding initiatives that focus on improving French beans in Kenya.