Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes

Abstract

The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

Figure 1.

Genetic linkage maps obtained for AF5, BF6, and TF6 populations. The linkage groups in the AF5, BF6, and TF6 maps are indicated by AA, BB, and TA or TB, respectively, and the homoeologous groups are prefixed with HGs. Homologous or homoeologous marker loci are connected by lines.

Figure 2.

Comparison of the integrated consensus tetraploid Arachis map with diploid maps. The abbreviations AA and BB indicate LGs on the AF5 and BF6 maps, respectively, and the prefixes A and B show LGs on the integrated consensus map. Horizontal lines on the LGs indicate the positions of the mapped loci; the loci derived from one, two, three, four, five, and more than five genetic linkage maps are shown in black, blue, light blue, green, yellow, and red. Vertical bars on the left side of the LGs indicate the locus clusters. Homologous and homoeologous loci are connected by black lines.

Figure 3.

Comparative maps of Arachis and four other legumes, C. cajan, G. max, L. japonicus, and M. truncatula. Circled bars in brown, magenta, green, yellow, and blue indicate the genomes of Arachis, C. cajan (A), G. max (B), L. japonicus (C), and M. truncatula (D), respectively. Homologous loci are connected by lines.