Genetic Studies and Mapping of Beneficial Alleles from Wild Species to Improve Agronomic Traits in Cultivated Groundnut (Arachis Hypogaea L.)

Abstract

Groundnut (Arachis hypogaea L.) is a legume widely cultivated in tropical and sub-tropical regions. Although Senegal is among the largest African producers, yield has declined over the years. The narrow genetic diversity of the cultivated groundnut due to its monophyletic origin coupled with polyploidization has slowed down its genetic improvement using molecular tools. Wild species of groundnut are important sources of useful alleles that can be used to broaden the genetic base of the cultivated groundnut. However because of their inferior agronomic value, groundnut wild species have been little used to improve agronomic traits. Thus the present study was undertaken to enlarge the genetic diversity of cultivated groundnut and to estimate the relative contribution of the wild species to improve agronomic traits in cultivated groundnut. Specifically the objectives were to: i) identify the main constraints that farmers are facing in groundnut production and their varietal traits preferences; ii) identify promising breeding lines; iii) identify genomic regions that underlie the variation of the observed phenotypes and iv) evaluate the increase of the phenotypic value associated with the alleles of the wild species. A participatory rural appraisal (PRA) was conducted using focus group discussions (FGD) and questionnaires in three regions (Kaolack, Kaffrine and Tambacounda). Furthermore, an advanced backcross BC2F4:6 mapping population was developed at CERAAS (centre d’etudes regional pour l’amelioration de l’adaptation a la secheresse) from a cross between Fleur11 used as recurrent parent and a synthetic allotetraploid donor ISATGR52B (A. duranensis (AA) x A. valida (BB)) 4x. Two hundred BC2F4 families from this cross were genotyped with 128 microsatellite markers (SSRs) at the genotyping lab (CERAAS) and the BC2F4:6 progenies plus Fleur11 were evaluated in four different environments. The PRA study revealed that groundnut remained the main cash crop cultivated by farmers. Farmers were ready to adopt varieties that have high pod and haulm yield and large pod and seed size regardless of oil content. The main constraints highlighted by farmers were marketability and access to land. However drought was the constraint that farmers identified as the most important and that could be addressed by breeders. A large phenotypic variation was observed between the advanced backcross (AB) lines. The interaction between genotypes and environments was significant. The analysis performed in each site allowed selecting fifty lines based on the weight attributed to each target trait using the selection index. Among the fifty lines, eleven were constantly present across sites. The GGE biplot identified B7_32_8_1 and Fleur11 as the best performing lines in terms of pod yield. The genotyping analysis conducted on the BC1 progenies permitted the construction of a genetic linkage map which spanned a cumulative length of 1792 cM with an average marker density of 6.4 cM. Three hundred and thirty loci were mapped onto 20 linkage groups (LGs). The quantitative trait loci (QTL) analysis conducted with the genotyping and phenotyping data of the BC2F4:6 families revealed 38 QTL related to agronomical traits. Most of the identified QTL for seed related traits were located on LG B3. For 50% of the identified QTL, the wild alleles contributed positively to the variation of the trait. Five QTL (5) were newly mapped. For 4 out of the 5 QTL, increase of the phenotypic value was associated with the alleles of the wild parent. The QTL for undesirable traits from the wild species (deep pod constriction, pronounced pod beak and spread growth habit) were also mapped and markers linked to them identified. This study has demonstrated the potential of alleles from wild relatives to enrich the genetic base of cultivated groundnut and to improve agronomic traits.