An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

Gautami, Bhimana; Foncéka, Daniel; Pandey, Manish K.; Moretzsohn, Márcio de Carvalho; Sujay, V.; Qin, Hongde; Hong, Yanbin; Faye, Issa; Chen, Xiaoping; Amindala, BhanuPrakash; Shah, Trushar; Gowda, M. V. C.; Nigam, S. N.; Liang, Xuanqiang; Hoisington, D A; Guo, Bao‐Zhu; Bertioli, David J.; Rami, Jean-François; Varshney, Rajeev K.

doi:10.1371/journal.pone.0041213

Cited by 94 publications

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“…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.…”

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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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“…1 and 2, and Supplementary Figs. 1-12) and were numbered according to previously published linkage maps 17,19,23,24 . They represent 82% and 86% of the genomes, respectively, when considering genome size estimates based on flow cytometry 14,25 , or 95% and 98% of the genomes when using estimates derived from k-mer frequencies with k = 17 ( Supplementary Figs.…”

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

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“…Nowadays, hundreds or thousands of widely distributed SNPs and their positions in the genome (provide the reference genome is accessible) can be identified in a relatively short period of time and at a low cost. Thereby, in recent years, the number of molecular markers and, therefore, map resolutions have increased, which ultimately leads to the reduction of QTL interval lengths to a few cM (Gautami et al, 2012;Stephens et al, 2014;Soto et al, 2015).…”

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Unraveling the molecules hidden in the gray shadows of quantitative disease resistance to pathogens

2018

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One of the most challenging questions in plant breeding and molecular plant pathology research is what are the genetic and molecular bases of quantitative disease resistance (QDR)?. The scarce knowledge of how this type of resistance works has hindered plant breeders to fully take advantage of it. To overcome these obstacles new methodologies for the study of quantitative traits have been developed. Approaches such as genetic mapping, identification of quantitative trait loci (QTL) and association mapping, including candidate gene approach and genome wide association studies, have been historically undertaken to dissect quantitative traits and therefore to study QDR. Additionally, great advances in quantitative phenotypic data collection have been provided to improve these analyses. Recently, genes associated to QDR have been cloned, leading to new hypothesis concerning the molecular bases of this type of resistance. In this review we present the more recent advances about QDR and corresponding application, which have allowed postulating new ideas that can help to construct new QDR models. Some of the hypotheses presented here as possible explanations for QDR are related to the expression level and alternative splicing of some defense-related genes expression, the action of "weak alleles" of R genes, the presence of allelic variants in genes involved in the defense response and a central role of kinases or pseudokinases. With the information recapitulated in this review it is possible to conclude that the conceptual distinction between qualitative and quantitative resistance may be questioned since both share important components. Keywords: breeding, complex traits, genome, gene expression, plant immunity, quantitative disease resistance (QDR), quantitative trait loci (QTL). RESUMENUna de las preguntas más desafiantes del fitomejoramiento y de la fitopatología molecular es ¿cuáles son las bases genéticas y moleculares de la resistencia cuantitativa a enfermedades?. El escaso conocimiento de cómo este tipo de resistencia funciona ha obstaculizado que los fitomejoradores la aprovecharlo plenamente. Para superar estos obstáculos se han desarrollado nuevas metodologías para el estudio de rasgos cuantitativos. Los enfoques como el mapeo genético, la identificación de loci de rasgos cuantitativos (QTL) y el mapeo por asociaciones, incluyendo el enfoque de genes candidatos y los estudios de asociación amplia del genoma, se han llevado a cabo históricamente para describir rasgos cuantitativos y por lo tanto para estudiar QDR. Además, se han proporcionado grandes avances en la obtención de datos fenotípicos cuantitativos para mejorar estos análisis. Recientemente, algunos genes asociados a QDR han sido clonados, lo que conduce a nuevas hipótesis sobre las bases moleculares de este tipo de resistencia. En esta revisión presentamos los avances más recientes sobre QDR y la correspondiente aplicación, que han permitido postular nuevas ideas que pueden ayudar a construir nuevos modelos. Algunas de las hipótesis presen...

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“…More interestingly, this reference consensus genetic map was divided into 203 sets of 20 cM bins, each which carry one to 20 loci with an average of four marker loci per bin. Furthermore, soon after the first dense consensus map published by Gautami et al (2012b), another joint international research effort has resulted in a much improved consensus genetic map based on 16 mapping populations. The mapping information from five new genetic maps were utilized for improvement of the earlier consensus map from 897 marker loci to 3693 marker loci spanning 2651 cM of the genome and 20 linkage groups (Shirasawa et al, 2013).…”

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Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.Key Words: Arachis hypogaea, Arachis species, genomics, genetic maps, molecular markers, molecular breeding, Peanut Genome Consortium (PGC).The world's population is predicted to reach nine billion by 2050 (Nature Editorial, 2010), which means greater demand for food, hence, a continuing need to produce improved cultivars of crop plants. Advances in food production will require greater efforts in agricultural research to increase crop yield with improved genetics for plant protection from biotic and abiotic stresses. Agricultural biotechnology is one tool that holds great promise for sustainability of agricultural production and feeding an ever increasing population.Peanut (Arachis hypogaea L.), or groundnut, is one of the major economically important legumes that is cultivated worldwide for its ability to grow in semi-arid environments with relatively low inputs of chemical fertilizers. On a global basis, peanut also is a major source of protein and vegetable oil for human nutrition, containing about 28% protein, 50% oil and 18% carbohydrates. Peanut is cultivated in more than 100 countries in Asia, Africa and the Americas, grown mostly by resource-limited farmers of the semi-arid regions. India and China together produce almost twothirds of the world's peanuts, and the U...

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An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

Cited by 94 publications

References 43 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

Unraveling the molecules hidden in the gray shadows of quantitative disease resistance to pathogens

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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