Genomic resources, interspecific introgression and trait dissection in Groundnut

Among the numerous interactions and collaborations between researchers from Brazil and from France, facilitated by the Labex under the CIBA consortium umbrella, the one on groundnut improvement has emblematic features. This is a programme aimed at developing genome analysis and genetic improvement in a species of South American origin that has become very important for many economies and populations in Asia and Africa. It emerged from a single event of allotetraploidization that gave rise to a cultivated species with a limited whole range of variation. The research conducted encompassed two components: one consisted in developing genomic resources as a foundation for genome analysis; the other consisted in a base?broadening scheme development starting from a cross between a synthetic amphidiploid made at Embrapa and an improved groundnut variety cultivated in Senegal. The first component involved a stay of scientists from Embrapa at Cirad in Montpellier for the production of large genomic segments in Bacterial Artificial Chromosomes (BAC); BAC libraries were produced from the ancestral species, which became a useful resource for a broader community within the GCP. It is still being used for basic genomic studies. The second component, which will be described in more details, involved a PhD/postdoc work at Cirad and breeding activities conducted at ISRA/CERAAS in Sénégal. The hybrid between the synthetic amphidiploid and the cultivar was used to initiate a large marker assisted backcross scheme and develop a collection of chromosome segment substitution lines (CSSLs) that would globally incorporate the whole genome of the wild ancestors (the "donor") as overlapping segments introgressed in the "recipient" cultivar. As such, they enable characterization of the specific phenotypic effect of allelic replacement on the substituted segment, considerably limiting the confusing effects of epistasis with the rest of the genome. Reciprocally, they enable characterization of the pleiotropic effect of donor genes (or stretches of genes). They enable the breeder to assess the value per se and to test various combinations of donor genome segments in the recipient genome. This has been very successful and is currently producing novel materials with high genetic resolution capacity and high breeding value. These studies have received financial support from the Generation Challenge Programme (GCP). (Résumé d'auteur

Genetic mapping and synteny analysis allowed the identification of genome rearrangements in the allotetraploid Arachis hypogaea

Cultivated peanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid AABB (2n = 4x = 40) originated from a recent and single hybridization event between two wild diploids. Among the sixty wild species described, A. duranensis (AA) and A. ipaensis (BB) appeared to be the best candidates for the A and B genome donors, respectively. The combining effects of polyploidisation and domestication have greatly narrowed the genetic diversity and hampered the application of molecular approaches for the genetic analysis and the improvement of the cultivated peanut. Recently, the development of synthetic amphidiploids using wild diploid species allowed overcoming the reproductive barrier between wild diploids and the cultivated tetraploid species. This material is an important resource for genetic mapping, synteny analysis between the A and B genomes and molecular breeding. The objectives of this study were to construct a wild x cultivated tetraploid genetic map using the co-dominant SSR markers, to assess the type of inheritance and the synteny between the A and B genomes. A synthetic amphidiploid, obtained from the cross between the most probable wild progenitors of the cultivated peanut (A. duranensis, A ipaensis), was crossed to the Fleur11 variety. A population of 88 BC1F1 individuals was produced and genotyped with 277 polymorphic SSR markers. We mapped 299 loci in 21 linkage groups (LGs), spanning a total map distance of 1843.7 cM. We determined the sub-genomic origin of the SSR alleles by comparison with the alleles of the wild diploid parents of the amphidiploid. This enabled us to confirm the disomic inheritance of all loci and to distinguish the A from the B genome linkage groups (LG). We have not observed LGs with mosaic A/B allele composition. This indicates that the chromosome pairing happened between "homologous" genomes and confirms the high affinity between the A/B genomes of the cultivated species and the A genome of A. duranensis and the B genome of A. ipaensis, respectively. We also identified the homeologous LGs with 53 SSR markers that mapped on both the A and B genomes. We observed an overall good collinearity between each pair of homeologous LGs. However, three inversions of chromosome segment were pointed out between homeologous LGs a01/b01, a03/b03 and a09/b09, as well as a major translocation involving the LGs b07 and b08. These rearrangement events are discussed regarding the divergence of the A and B genomes. The result of this study contributes to the comprehension of the structure of the A and B genomes and the broadening of the gene pool of the cultivated peanut. (Texte intégral

Elargissement de la base génétique de l'arachide cultivée (Arachis hypogaea) : applications pour la construction de populations, l'identification de QTL et l'amélioration de l'espèce cultivée

L'arachide (Arachis hypogaea L.) est une plante allotétraploïde (2n = 4x = 40) issue d'un événement récent d'hybridation entre deux espèces sauvages suivi d'un doublement spontané des chromosomes. La variabilité génétique existant dans le compartiment cultivé est faible. Les espèces diploïdes sauvages apparentées à l'arachide cultivée représentent un important réservoir d'allèles nouveaux utilisables pour élargir le pool génique du cultigène. L'objectif général de cette thèse est d'augmenter les marges de progression en amélioration de l'arachide par recours aux ressources génétiques sauvages. Nous avons développé une population BC1F1 à partir du croisement entre Fleur11 et un amphidiploïde synthétique (A. ipaensis x A. duranensis)x4 qui associe les génomes des plus probables progéniteurs sauvages de l'espèce cultivée. Nous avons d'abord construit une carte génétique comprenant 298 loci positionnés sur 21 groupes de liaison avec une taille totale de 1843.7 cM. Nous avons ensuite conduit une analyse AB-QTL pour plusieurs caractères impliqués dans la productivité, l'adaptation et la domestication de l'arachide. Au total, nous avons cartographié 95 QTL. Pour plusieurs QTL, les effets positifs sont associés aux allèles provenant des espèces sauvages. Nous avons aussi identifié trois régions du génome qui portent des empreintes de la domestication. Nous avons enfin développé une population de 122 lignées d'introgression à l'aide d'une stratégie de sélection assistée par marqueurs. L'ensemble des groupes de liaison sont couverts avec des fragments chevauchants, issus des donneurs sauvages, d'une taille moyenne de 39.2 cM et chaque lignée comprend en moyenne 1.2 fragments. Nous avons par ailleurs discuté l'utilisation de cette collection de lignées d'introgression pour des applications de sélection et de génétique. Nos résultats ouvrent de nouvelles perspectives pour l'amélioration de l'arachide par croisement avec les espèces sauvages apparentées.(Résumé d'auteur

Interspecific introgression and trait dissection in peanut (Arachis hypogaea) : W336

Cultivated peanut is originating from South-America and has become very important for many economies and populations in Asia and Africa. It emerged from a single event of allotetraploidization that gave rise to a limited diversity at the DNA level. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using a synthetic amphidiploid as donor parent new interspecific populations have been developed with an improved variety cultivated in Senegal. An advanced backcross (AB-QTL) population was first used to conduct a QTL study for several traits involved in peanut productivity and adaptation. A total of 95 QTLs were detected, about half of them showing positive effects associated with the wild allele. We then produced a set of 122 Chromosome Segment Substitution Lines (CSSL) that globally incorporate the whole genome of the wild donor as overlapping segments introgressed in the recipient cultivar. As a demonstration of the utility of these lines, four morphological traits were evaluated on a subset of 80 CSSLs. A detailed analysis of one of these traits, plant growth habit, showed that it is complex and governed by several QTLs with various effects. The comparison of the number of QTLs mapped for growth habit between CSSLs and AB-QTL showed the higher efficiency of the CSSL population and its interest for QTLs validation, breeding and gene discovery. (Résumé d'auteur

Assessment of the variability of Senegalese landraces for phenology and sugar yield components to broaden the genetic pool of multi-purpose sorghum

Sweet sorghum is highly coveted to contribute and take up food and energy challenges. A collection of 84 West Africa landraces mostly from Senegal and four control cultivars were screened to identify relevant accessions and trait combination for multi-purpose (sugar/grain/biomass). The implication of photoperiod sensitivity was particularly addressed. A total of 20 traits related to phenology, morphology, grain and sugar production were assessed in two sowing dates (July and August) at CNRA Bambey in Senegal. Late sowing resulted in shortened vegetative phase and a significant decrease in traits related to plant size, stem sugar, biomass and grain productions. Broad-sense heritability was moderate to high for most of the phenology, morphology, grain and sugar-related traits, suggesting their interest for breeding. All the traits related to plant size were positively correlated with plant sugar production except plant height. A cluster analysis identified three groups contrasting in their ability to combine sugar, grain or fodder production based on 18 traits measured for the early sowing. Clusters I and III were suitable for one purpose: grain and sugar, respectively. Cluster II was the most suitable for multi-purpose, showing the best trade-off among grain, sugar and vegetative biomass production. The best accessions for stem sugar yield belonged to durra, caudatum and their intermediate types. The relationship between internode size and sweetness should be further studied, in particular exploring their relationship with internode tissue anatomy. Further studies are also needed to evaluate the role that stay-green can play in sugar yield maintenance under post-flowering drought. (Résumé d'auteur

Evidence of mixed disomic and polysomic inheritance in allotetraploid peanut. [P1034]

Cultivated peanut and wild synthetic are allotetraploid (2n=4x=40) with two homeologous sets of chromosomes. Genetic mapping in tetraploid peanut is usually performed considering a diploid-like meiotic behavior. However, a recent study points out the occurrence of partial tetrasomic behavior. In this study, we investigated the meiotic inheritance of the allotetraploid peanut using 380 SSR markers and 93 F2 progenies derived from the cross between Arachis hypogaea cv Fleur11 (AABB) and ISATGR278/18 (AAKK), a wild synthetic with a K genome reported to pair with the cultivated B genome during meiosis. As results, the analysis of the segregation for 34 SSR markers, revealed unexpected null band among some progenies, unexplainable under disomic inheritance. Chi-square tests for these loci indicated a 1:34:1 segregation ratio consistent with a tetrasomic inheritance rather than the 1:2:1 Mendelian ratio for disomic inheritance. A linkage map was constructed. It consists of 365 loci aligned into 20 linkage groups (LGs) with a total length of 1928 cM, averaging 5.1 cM between markers. Interestingly, among the ten homeologous sets of LGs, one set consisted of markers that all segregate in a tetrasomic pattern, 6 in a likely disomic pattern and the 3 remaining in a mixed pattern with disomic and tetrasomic loci, clustered on the same LG. Our findings provided evidence that the meiotic behavior of allotetraploid peanut is neither fully disomic nor fully tetrasomic, but rather mixed. In addition, we reported a conversion of homeologous chromosomes for some progenies. This opens new horizons for peanut breeding. (Texte intégral

Inheritance of fresh seed dormancy in Spanish-type peanut (Arachis hypogaea L.): Bias introduced by inadvertent selfed flowers as revealed by microsatellite markers control

Production and seed quality in peanut (Arachis hypogaea L.) can be reduced substantially by in situ germination under unpredictable rainfed environments. Inheritance of fresh seed dormancy in Spanish x Spanish crosses was studied with two sets of segregating populations, an F2 population derived from true F1 hybrids identified with peanut microsatellites markers and other populations (F2, BC1P1S and BC1P2S) from randomly-selected F1 individuals. In the F2 population developed with true F1 hybrids, the chi square test was not significant for the deviation from the expected 3:1 (dormant: non-dormant) ratio. In addition, the bimodal frequency distribution curve with the F2 population gave more evidence that fresh seed dormancy is controlled by a single dominant gene. The average frequency (48%) of true F1 hybrids give evidence that deviations from expected ratios in the populations (F2 and BC1P1S) developed from non-tested F1 individuals, is most likely due to inadvertent selfs. This study emphasized the need to identify with molecular markers the cross progenies in self-pollinated crops as peanut before testing for any trait. (Résumé d'auteur