Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut. A r t i c l e s npg © 2016 Nature America, Inc. All rights reserved.Nature GeNetics VOLUME 48 | NUMBER 4 | APRIL 2016 4 3 9 subgenomes of A. hypogaea. 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. RESULTS Sequencing and assembly of the diploid A and B genomesConsidering that A. duranensis V14167 and A. ipaensis K30076 are likely good representatives of the ancestral species of A. hypogaea, we sequenced their genomes. After filtering, the data generated from the seven paired-end libraries corresponded to an estimated 154× and 163× base-pair coverage for A. duranensis and A. ipaensis, respectively (Supplementary Tables 1-6). The total assembly sizes were 1,211 and 1,512 Mb for A. duranensis and A. ipaensis, respectively, of which 1,081 and 1,371 Mb were represented in scaffolds of 10 kb or greater in size (Supplementary Table 7). Ultradense genetic maps were generated through genotyping by sequencing (GBS) of two diploid recombinant inbred line (RIL) populations (Supplementary Data Set 1). SNPs within scaffolds were used to validate the assemblies and confirmed their high quality; 190 of 1,297 initial scaffolds of A. duranensis and 49 of 353 initial scaffolds of A. ipaensis were identified as chimeric, on the basis of the presence of diagnostic population-wide switches in genotype calls occurring at the point of misjoin. Chimeric scaffolds were split, and their components were remapped. Thus, approximate chromosomal placements were obtained for 1,692 and 459 genetically verified scaffolds, respectively. Conventional molecular marker maps (Supplementary Data Set 2) and syntenic inferences were then used to refine the ordering of scaffolds within the initial genetic bins. Generally, agreement was good for maps in euchromatic arms and poorer in pericentromeric regions (although one map 22 showed large inversions in two lin...

Nuclear restriction fragment length polymorphism (RFLP) analysis was used to determine the wild diploid Arachis species that hybridized to form tetraploid domesticated peanut. Results using 20 previously mapped cDNA clones strongly indicated A. duranensis as the progenitor of the A genome of domesticated peanut and A. ipaensis as the B genome parent. A large amount of RFLP variability was found among the various accessions of A. duranensis, and accessions most similar to the A genome of cultivated peanut were identified. Chloroplast DNA RFLP analysis determined that A. duranensis was the female parent of the original hybridization event. Domesticated peanut is known to have one genome with a distinctly smaller pair of chromosomes (“A”), and one genome that lacks this pair. Cytogenetic analysis demonstrated that A. duranensis has a pair of “A” chromosomes, and A. ipaensis does not. The cytogenetic evidence is thus consistent with the RFLP evidence concerning the identity of the progenitors. RFLP and cytogenetic evidence indicate a single origin for domesticated peanut in Northern Argentina or Southern Bolivia, followed by diversification under the influence of cultivation.

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The cultivated peanut (Arachis hypogaea L.) is an allotetraploid species with a very large and complex genome. This species is susceptible to numerous foliar and soil‐borne diseases for which only moderate levels of resistance have been identified in the germplasm collection, but several of the 81 wild species are extremely resistant to many destructive peanut diseases. Peanut species were grouped into nine sections, but only taxa in section Arachis will hybridize with A. hypogaea. Most of these species are diploid, but two aneuploids and two tetraploids also exist in the section. The first peanut cultivars released after interspecific hybridization were ‘Spancross’ and ‘Tamnut 74’ during the 1970s from a cross between A. hypogaea and its tetraploid progenitor. However, introgression of useful genes from diploids has been difficult due to sterility barriers resulting from genomic and ploidy differences. To utilize diploids in section Arachis, direct hybrids have been made between A. hypogaea and diploid species, the chromosome number doubled to the hexaploid level, and then tetraploids recovered with resistances to nematodes, leaf spots, rust, and numerous insect pests. ‘Bailey’, a widely grown Virginia‐type peanut, was released from these materials, and other cultivars are gown in Asia and South America. Alternatively, hybrids between diploid A and B genome species have been made, the chromosome number doubled, and cultivars released with nematode resistance derived from Arachis species. Introgression from Arachis species to A. hypogaea appears to be in large blocks rather than as single genes, and new genotyping strategies should enhance utilization of wild peanut genetic resources.

Peanut germ plasm consists of the cultivated allotetraploid species Arachis hypogaea L. and a large number of wild species, which are nearly all diploids. Our previous work indicated a very low level of genetic variability in American cultivars, as assayed by restriction fragment length polymorphism (RFLP) analysis. Since American cultivars might represent a narrow genetic base, we expanded our study to include unadapted germ-plasm lines from the various South American centers of origin, Africa, and China, where considerable morphological and physiological variability has been reported to exist. Wild species of section Arachis were included in the evaluations since they show a high degree of variation when assayed by RFLPs. Three methods were used to assay for RFLP variation: (i) conventional RFLP analysis using random genomic clones from peanut and cDNA clones from peanut and alfalfa (Medicago sativa); (ii) polymerase chain reaction (PCR) amplification of random primer sequences; (iii) four-cutter analysis of PCR-amplified fragments. In all cases a very low level of variability was found in cultivated peanut, while abundant variability was present among wild diploid species. The results are discussed in terms of peanut evolution and significance to peanut breeding.Key words: polymerase chain reaction, Arachis hypogaea, restriction fragment length polymorphism.

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