Genetic and geographic origin of domesticated peanut as evidenced by 5S rDNA and chloroplast DNA sequences

Grabiele, Marina; Chalup, Laura; Robledo, Germán; Seijo, Guillermo

doi:10.1007/s00606-012-0627-3

Cited by 77 publications

(73 citation statements)

References 53 publications

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“…The earliest archeological records of Arachis cultivation are about 7,800 years old from Peru, far from the most likely region of origin for A. hypogaea or any natural Arachis species distribution 49 . It seems likely that Arachis cultivation would have started within the native range well before then 11,50 . The date of polyploidization is uncertain, but the earliest identifiable remains of A. hypogaea date from ~3,500-4,500 years ago 51 .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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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...

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Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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“…vulgaris (Krapovickas and Gregory, 1994). A recent molecular genetic study used a chloroplast sequence and the non-transcribed spacer of the nuclear 5S rDNA to decipher the origin of cultivated peanut (Grabiele et al, 2012): A. duranensis and A. ipaensis hybridized and gave rise to the wild tetraploid A. monticola, in northern Argentina. A. hypogaea was selected from A. monticola in northern Argentina and southern Bolivia, from where it was dispersed and diversified into two subspecies with six varieties, providing a clear example of a domestication event followed by diversification, as outlined by Meyer and Purugganan (2013).…”

Section: Peanutmentioning

confidence: 99%

Crop domestication in the upper Madeira River basin

Clement

Rodrigues

Alves‐Pereira

et al. 2016

Bol. Mus. Para. Emílio Goeldi. Ciênc. hum.

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Most native Amazonian crops were domesticated in the periphery of the basin. The upper Madeira River basin is an important part of this periphery where several important crops were domesticated and others are suspected to have been domesticated or arrived early. Some of these crops have been reasonably well studied, such as manioc, peanut, peach palm, coca and tobacco, while others are not as well known, such as the hot peppers Capsicum baccatum and C. frutescens, and still others need confirmation, such as cocoyam and annatto. We review the information available for manioc, peach palm, Capsicum, peanut, annatto and cocoyam. The state-of-the-art for Capsicum frutescens, annatto and cocoyam is insufficient to conclude definitively that they were domesticated in the upper Madeira, while all the others have at least one of their origins or centers of diversity in the upper Madeira. Keywords: Amazonian crops. Center of domestication. Crop domestication. Southwestern AmazoniaResumo: A maioria dos cultivos nativos da Amazônia foi domesticada na periferia da bacia. A bacia do alto rio Madeira é uma parte importante dessa periferia, onde se suspeita que vários cultivos importantes foram domesticados, alguns são confirmados e outros possivelmente chegaram há muito tempo na região. Alguns destes cultivos foram razoavelmente bem estudados, tais como mandioca, amendoim, pupunha, coca e tabaco, enquanto outros não são tão bem conhecidos, como as pimentas Capsicum baccatum e C. frutescens, e ainda outros precisam de confirmação, como taioba e urucum. Revisamos as informações disponíveis para a mandioca, pupunha, Capsicum, amendoim, urucum e taioba. O estado da arte de Capsicum frutescens, urucum e taioba é insuficiente para concluir definitivamente que eles foram domesticados no alto rio Madeira, enquanto todos os outros têm pelo menos uma das suas origens ou centros de diversidade na região.

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“…& W.C. Greg. (provider of the B genome) were found to be the parents of A. hypogaea (Fávero et al, 2006;Seijo et al, 2004Seijo et al, , 2007Grabiele et al, 2012). Identifying a species with high homology to the B genome of A. hypogaea is important because the success of introgression breeding programs greatly depends on the choice of a species with B genome compatibility with that of the peanut (Cunha et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Crossability of Arachis valida and B genome Arachis species

Wondracek-Lüdke

Custódio

Simpson³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The peanut (Arachis hypogaea) is an important food crop in much of the tropical and semi-tropical parts of the world. The peanut is an allotetraploid with an AABB genome formula derived from diploids A. duranensis (A genome) and A. ipaënsis (B genome). The success of an introgression program that aims to improve cultivated varieties of the peanut depends on whether the chosen B genome species is homologous with the B genome of the peanut. While not directly involved in the origin of the peanut to the best of our knowledge, Arachis valida is a B genome species that could potentially be a bridge species or a source of new and different alleles, because of its resistance to diseases and pests. In this study, we investigated the crossability of A. valida with five other B genome species of section Arachis. Eight cross-combinations were made with A. valida and A. gregoryi, A. ipaënsis, A. magna, A. valida, and A. williamsii. Two hundred and forty pollinations were made yielding 61 fruit segments, 61 seeds, one abortion, and 24 hybrid plants. An analysis of the morphological characteristics and pollen viability confirmed that the plants 17574-17586 (2015) were hybrids. Our results indicated that higher pollen viability of hybrid plants corresponded with higher affinity between parent plants used in crossings. This conclusion corroborates much of previous research carried out by many other authors in the past.

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Genetic and geographic origin of domesticated peanut as evidenced by 5S rDNA and chloroplast DNA sequences

Cited by 77 publications

References 53 publications

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

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

Crop domestication in the upper Madeira River basin

Crossability of Arachis valida and B genome Arachis species

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