RESUMEN
Family farms play an essential role in agroecological transition in Sahelian countries and worldwide. They present diversified features in terms of socio-economic organization, agrobiodiversity management and cropping systems diversity. Decentralized participatory breeding approaches aim to sustain the diversity of varieties adapted for such smallholder farmers' contexts. However the lack of clear target population of environments limits the focus and the efficiency of these approaches given the large diversification of the local contexts. In this study, we surveyed variables linked to agrosystems, crop management options and farmers' criteria of varietal evaluation from 254 family farms sampled along 13 locations spanning the target area of a decentralized participatory breeding program of cowpea crop (Vigna unguiculata L. Walp) in Niger. The objective of our study was to infer typologies of family farms in the study area based on relevant variables supporting the setting of target population of environments (TPEs) to be considered in the breeding program. We used factorial analysis of mixed data (FAMD) and the Discriminant Analysis of Principal Components (DAPC) to infer the clusters. Chi square test, analysis of variance and generalized linear model were used to identify key variables discriminating the clusters. These clusters were geographically mapped to analyze their multilocal distribution. So, we identified and characterized four clusters structuring the diversity of the local agrosystems (Typologie G), five clusters structuring the diversity of cowpea cropping management options (Typologie C) and five clusters structuring the diversity of criteria used by farmers to evaluate the performance of cowpea varieties in the local contexts (Typologie P). Typology G distinguished farms based on discriminating variables linked for instance to secondary activities, cultivated species, soil fertility management practices and farm resources including land and livestock. Typology C distinguished farms based on cowpea management pratices including the secondary crop intercropped with cowpea (sorghum, Guinea sorrel, sesame or groundnut) and the use of cowpea harvest products (seeds, haulms, hulls). Typology P was based on discriminating performance criteria including cycle length, insect resistance, striga resistance, drought resistance, haulm production and economic value of cowpea variety. This methodology provides a robust and replicable way for the definition of clusters capturing the diversity of farms and local contexts. We discussed the perspective of using these clusters to set target population of environments for decentralized breeding programs.
RESUMEN
BACKGROUND: Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the previously detected root-related trait genes in maize were new without functional verification. In this study, seven seedling root architectural traits were examined at three developmental stages in a recombinant inbred line population (RIL) of 179 RILs and a genome-wide association study (GWAS) panel of 80 elite inbred maize lines through quantitative trait loci (QTL) mapping and genome-wide association study. RESULTS: Using inclusive composite interval mapping, 8 QTLs accounting for 6.44-8.83 % of the phenotypic variation in root traits, were detected on chromosomes 1 (qRDWv3-1-1 and qRDW/SDWv3-1-1), 2 (qRBNv1-2-1), 4 (qSUAv1-4-1, qSUAv2-4-1, and qROVv2-4-1), and 10 (qTRLv1-10-1, qRBNv1-10-1). GWAS analysis involved three models (EMMAX, FarmCPU, and MLM) for a set of 1,490,007 high-quality single nucleotide polymorphisms (SNPs) obtained via whole genome next-generation sequencing (NGS). Overall, 53 significant SNPs with a phenotypic contribution rate ranging from 5.10 to 30.2 % and spread all over the ten maize chromosomes exhibited associations with the seven root traits. 17 SNPs were repeatedly detected from at least two growth stages, with several SNPs associated with multiple traits stably identified at all evaluated stages. Within the average linkage disequilibrium (LD) distance of 5.2 kb for the significant SNPs, 46 candidate genes harboring substantial SNPs were identified. Five potential genes viz. Zm00001d038676, Zm00001d015379, Zm00001d018496, Zm00001d050783, and Zm00001d017751 were verified for expression levels using maize accessions with extreme root branching differences from the GWAS panel and the RIL population. The results showed significantly (P < 0.001) different expression levels between the outer materials in both panels and at all considered growth stages. CONCLUSIONS: This study provides a key reference for uncovering the complex genetic mechanism of root development and genetic enhancement of maize root system architecture, thus supporting the breeding of high-yielding maize varieties with propitious root systems.