Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid

Abstract

BackgroundPeanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis.ResultsTwo hundred ninety eight (298) loci were mapped in 21 linkage groups (LGs), spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor segment with the best possible return to the background of the cultivated variety provided a set of lines offering an optimal distribution of the wild introgressions.ConclusionThe genetic map developed, allowed the synteny analysis of the A and B genomes, the comparison with diploid and tetraploid maps and the analysis of the introgression segments from the wild synthetic into the background of a cultivated variety. The material we have produced in this study should facilitate the development of advanced backcross and CSSL breeding populations for the improvement of cultivated peanut.

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

“…Progeny are vigorous, phenotypically normal and fertile and showed lower segregation distortion 16,17 than has been observed for some populations derived from A. hypogaea intraspecific crosses [18][19][20][21] . Therefore, as a first step to characterizing the genome of cultivated peanut, we sequenced and analyzed the genomes of the two diploid ancestors of cultivated peanut.…”

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

“…Additional markers were obtained from Hong et al (2008) and Foncéka et al (2009) after creating consensus linkage groups (LGs) using the Comparative Map and Trait Viewer (CMTV) tool version 1.1 (Sawkins et al 2004). A total of 32 primer pairs were successfully scored on all the 96 genotypes used in the present study (Table 2).…”

“…A total of 32 primer pairs were successfully scored on all the 96 genotypes used in the present study (Table 2). The 32 primer pairs amplified a total of 392 SSR marker bands and covered a total of about 500 cM distance of the genetic linkage map, which is close to 25% of the peanut genome based on Burow et al (2001) and Foncéka et al (2009). The consensus LG2 and LG8 had 8 and 4 primers each, LG3, LG4, LG6, LG7 and LG11 had 3 primers each, LG1, LG9, LG10 and LG13 had one primer each, and 3 unmapped primers were used ( Table 2).…”

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…Establishment of such a permanent introgression library with characterized genomic fragments of wild crop relatives in a defined genetic background will allow phenotypic characterization of an unlimited number of target traits, which, coupled with molecular tools, will provide a means of final gene identification and their subsequent incorporation, pyramiding in desired genotypes, ultimately leading to better performing commercial cultivars. So far, not many such series of lines have been developed in grain legumes, but there are several ongoing efforts to establish them in pea (Smýkal and Kosterin, 2010;Smýkal et al, unpublished), beans (Muñoz et al, 2004;Blair et al, 2006;Blair and Izquierdo, 2012), groundnut (Foncéka et al, 2009) and other legumes (reviewed in Upadhyaya et al, 2011). Intergeneric legume hybrids have been critically reviewed in McComb (1975), which found insufficient evidence for all reported crosses due to misleading paper titles, confusion of vegetative with generic hybrids, the occurrence of patrocliny, and the frequent occurrence of misplaced generic boundaries.…”