Genetic variability, path coefficient and marker-trait association analysis for resistance to rosette disease in groundnut.

Abstract

Several abiotic, biotic and socio-economic aspects constrain the production of groundnut (Arachis hypogea L.). Groundnut rosette disease (GRD) which can cause yield losses of up to 100% in susceptible cultivars, is among the most important biotic stresses. The use of resistant cultivars is the most viable method to control the disease, therefore, breeding for high yielding and GRD resistant cultivars is needed and should be a priority. The present study was conducted to: (i) determine genetic variability for GRD response and yield traits in selected groundnut accessions under natural infestation, (ii) assess the relationship between seed yield and its related traits, and analyse agro-morphological diversity in selected groundnut accessions under natural GRD infestation and (iii) evaluate groundnut recombinant inbred lines for resistance to GRD and perform SNP marker-trait association analysis. Twentyfive groundnut accessions and three controls were evaluated under natural GRD infestation to assess genetic variability for GRD response and yield related traits. Seed yield, number of pods per plant, plant height, GRD incidence and number of secondary branches showed high phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV), while moderate variation (PCV and GCV) was observed for days to flowering and pod width. A combination of high heritability and genetic advance was recorded for number of secondary branches, plant height, seed yield and GRD incidence, indicating that phenotypic selection based on the mean would be successful in improving these traits. Phenotypic correlations and sequential path analysis indicated that high seed yield was directly associated with taller genotypes, higher number of pods per plant and hundred seed weight, which were a result of higher pod width and lower GRD incidence. Based on morphological traits, the evaluated accessions were grouped into four clusters. Days to flowering and maturity, number of branches, plant height, number of pods per plant, pod width and length, seed yield and GRD incidence, largely influenced this variation. Principal component analysis (PCA) biplot was effective in showing the genetic distance among the accessions with results consistent to those of the cluster analysis. Moreover, Shannon-Weaver diversity indices (0.949-0.9996) for qualitative traits also indicated the existence of high diversity among the accessions. A total of 25 groundnut genotypes, which comprised 21 RILs derived from a bi-parental cross, both parents, and two susceptible controls (CG7 and JL24) were evaluated and used to perform SNP marker-trait association analysis for resistance to GRD. There were significant differences among the lines in all recorded traits, indicating the existence of genetic variability and possibility of effective selection. Interaction of genotype and environment was significant for disease incidence and the glasshouse environment had higher disease pressure, providing the best discrimination among the tested genotypes. ICGV-SM 15605, ICGV-SM 15621, ICGV-SM 15618, ICGV-SM 15604 and ICGV-SM 15615 were among the resistant and high yielding RILs. Twenty-two highly significant marker-trait associations were identified, which will add to previously reported genomic regions influencing GRD and the aphid vector resistance. Overall, the study showed that taller genotypes, higher number of pods per plant and hundred seed weight can be used to improve seed yield in groundnut, particularly under GRD infestation. The genetic diversity among the accessions provides an opportunity for parent selection that can be used for breeding high yielding and GRD resistant cultivars. In addition, the SNP markers will be useful in classifying groundnut germplasm based on the GRD response and for their use in marker-assisted selection, once validated.