An alternation of generations means the plant, in this case the peanut, switches between the haploid (n) and diploid (2n) stages during its life. It is widely grown in the tropics and subtropics, being important to both small and large commercial producers. A total of 142 pre-selected common markers (Additional file 3: Table S1) meeting the selection criteria were added to the population-specific SNP markers for genetic linkage analysis using JoinMap v4.1 . A dotted line in LG11 indicates that SNP100024712 |F|0-54 marker has the best match position on Pv07; 45,623,999 bp with one insertion, one deletion and eight mismatched bases observed but not having any good match to Pv06 as expected from its flanking markers on the same linkage group. The developed map consists of 20 linkage groups and was 516 cM in length, based on 67 amplified fragment length polymorphism (AFLP) and one cross-species simple sequence repeat (SSR) marker, with the inter-marker distance varying from 4.7 to 32 cM. 20. The LOD score generated from IM mapping was then compared with the Genome Wide (GW) threshold at p ≤0.05 from the permutation test to be termed as ‘significant’. PubMed Google Scholar. In addition to these high quality markers chosen using a conventional mapping approach, a set of pre-selected common DArTseq markers having the following criteria were added during map construction; 1) polymorphic in the parental lines of both populations, 2) no more than five missing genotypes, 3) sequence mappable to the common bean, adzuki bean and mung bean genomes at high stringency (as described in Method). Of these two sets of high quality selected DArTseq markers, 268 out of 298 (89.9%) markers showed the expected segregation pattern (1:2:1 or 1:1) in the IA F2 segregating population and 611 out of 739 (82.7%) markers segregated in the expected pattern in the TD F3 population (3:2:3 or 3:5) at a significance level of p < 0.05. II. https://doi.org/10.1186/s12864-016-3393-8, DOI: https://doi.org/10.1186/s12864-016-3393-8. Only very recently were they bought together by a polyploidy event, probably in pre-historical times. Unweighted pair group method with arithmetic mean. has a more uniform karyotype. The inheritance of pod- and seed-number traits (PSNT) in peanut (Arachis hypogaea L.) is poorly understood. The putative synthetic blocks identified across legume genomes would facilitate more effective comparison of gene order in the legume species and assist in the identification of the location of genes underlying QTL involved in controlling agronomic and yield traits in bambara groundnut, facilitating the marker-assisted selection process. Underutilised and minor crops often have limited research or development funding with little or no interest from commercial seed companies. To illustrate our approach, we have located a significant internode length QTL in the TD F3 population with a LOD score of 5.3 to LG2 50.6 cM (CI: 47.6 – 53.2 cM), explaining 33.4% of phenotypic variation observed in this cross (listed in Table 2 and Fig. Dellaporta SL, Wood J, Hicks JB. Genetic analysis of soybean plant height, hypocotyl and internode lengths. Bhd., Setia Alam, Seksyen U13, 40170, Shah Alam, Selangor, Malaysia, Diversity Arrays Technology, Bldg 3, Lv D, University of Canberra, Kirinari St., Bruce, ACT 2617, Australia, You can also search for this author in Therefore, for cases where the genetic location and comparative syntenic position did not match with flanking markers, we manually used BLAST to determine whether the marker was likely to be a genuine breach of conserved synteny or whether other syntenic target sites might exist. This intraspecific map was constructed from 29 SSR and 209 DArT Array markers covering 608.6 cM in 21 linkage groups. Bi-allelic SNP markers were assigned as ‘a’, ‘h’ and ‘b’ as appropriate in each individual line according to the scoring pattern in both parental lines. Genome mapping and molecular breeding in plants — pulses, sugar and tuber. The number of groundnut accessions available in the gene banks has been reviewed by Pandey et al. The effect of soil moisture on the proximate composition of Bambara groundnut (Vigna subterranea (L.) Verdc). Vigna Angularis Sci Rep. 2015;5:8069. Question 34. 2014;46:707–13. The mapped location on Pv07 is at a genomic region flanked by AT rich sequences (496 bp and 392 bp apart upstream and downstream, respectively) and it could be mapped to the same chromosomes of adzuki bean and mung bean as the other 11 pre-selected markers on the same linkage group. Subsequently, the markers mappable to all three genomes were selected further for polymorphism between all parental lines and for not more than five missing data points per individual line. Cite this article. ante sequence information, but have closely related sequenced genome relatives. Nat Commun. HHC carried out the genetic mapping and QTL analysis. Three crops account for over 60% of all food calories grown in the world; wheat (Triticum spp. This has further allowed us to observe that soybean Internode Length 1–4 QTL falls within this bambara groundnut QTL conserved synteny region. Lavin M, Herendeen PS, Wojciechowski MF. J Sci Food Agric. Syst Biol. Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] The syntenic relationship of the bambara groundnut genetic map derived from two populations to common bean, adzuki bean and mung bean genomes is illustrated in Fig. The ability to translate trait information from model and major crops species to underutilised crops is important to be able to fully exploit available resources, effectively developing research simultaneously into a complex of species, rather than a single species in isolation. Manage cookies/Do not sell my data we use in the preference centre. Genome Res. Stadler F. Analysis of differential expression under water deficit stress and genetic diversity in Bambara groundnut (Vigna subterranea (L.) Verdc.) Ho, W.K., Chai, H.H., Kendabie, P. et al. The significance threshold of the LOD score was identified through permutation tests using 10,000 reiterations. Tree root identification saves ancient caves and the forest above them. c A simplified summary of the pseudo-physical map of bambara groundnut using the syntenic locus information from common bean (Pv), adzuki bean (Va) and mung bean (Vr) across the linkage groups of bambara groundnut genetic Map IA (based on chromosome number). Prior to MQM mapping, the closest linked marker to the QTL with significant LOD scores was selected as a co-factor. 10 c. 20 d. 30. This over-dependence on a limited number of major crops has narrowed the genetic and species base of agriculture. Both parental genotypes have significant contrasting features in growth habit and seed eye pattern. Individual mating patterns in mixed oak stands, annual production of around 38 million tonnes. The DNA from the Population TD was extracted following the Dellaporta method whereas column purification method was used for Population IA (DNeasy Plant Mini Kit, Qiagen) . A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. is widely grown as a plant protein source for poor farmers, particularly in sub-Saharan Africa with the seeds containing good levels of protein (18 to 26%) for human nutrition [3, 4]. 4a, b and c. From 11 linkage groups, four linkage groups (LG4, 8, 9 and 11 with LG9 being putative in adzuki bean genome due to a limited number of links) were found to map at the macro level to a single chromosome from each legume species. Convention of Biological Diversity (CBD). using novel high throughput Dissertation, Technische Universität München. All genotypic data were first analysed using a Chi-square test in JoinMap4.1 against the expected segregation patterns for the population and marker segregation type and for potential segregation distortion at a significance level of p <0.05. What's the chromosome number of peanut gamete? and W.C. Gregory and A. villosulicarpa Hoehne to mitotic chromosome analyses, Caryologia 54, no.4 4 (Jan 2014): 377–384. 2005;54:575–94. van Ooijen JW. A species tree constructed from the de novo transcriptomic assemblies of 22 accessions of 18 Vigna species has suggested that the divergence between bambara groundnut and other studied Vigna species is ~5 MYA except V. vexillata . The syntenic relationship between linkage groups of TD population through (a) pre-selected common markers or (b) pre-selected common markers and 26% population-specific markers mappable to common bean genome (each line indicates one syntenic location data). As this syntenic mapping approach is achieved through a cross-species comparison, we have been conservative in terms of mapping stringency so that the possibility of having more than one single good match location for a particular bambara groundnut marker sequence tag in the query genome was minimised. PubMed Bambara groundnut [Vigna subterranea (L) Verdc.] Bambara groundnut is cleistogamous, highly inbreeding and has 11 pairs of chromosomes (2n = 2x = 22) . and their syntenic relationships among closely related legumes. Or you can browse past editions. Bull Natl Plantentium. Silva LC, Cruz CD, Moreira MA, Barros EG. To receive your copy, sign up using the form below. PubMed The first intraspecific genetic map used a F3 segregating population (n = 73) derived from a cross between two domesticated forms of bambara groundnut (Tiga Nicuru and DipC), sharing the domesticated common parental line with the interspecific cross . 648 Broadway Skagway, AK 99840. A total of 156 and 597 population-specific SNP markers were used for the construction of the IA map and the TD map, respectively. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Wild relatives of crop species have been found to be potential sources of a number of deslra- ble characters, especially resistance to diseases and pests (Watson 1970; Knon and Dvorak 1976) The genus Arachis contains a number of such wtld Expl Agric. Our preliminary results overlaying the location of within-species QTL onto sequenced genomes suggests that translation of information (and the generation of gene lists within a trait controlling locus) can be used in an attempt to identify candidate controlling genes for further analysis within the species of interest which has no genome sequence. Seeds obtained from the colchine‐treated cuttings will all be semifertile AABB genome amphidiploids that can then be used as a male parent in crosses with A. hypogaea . Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. Bambara groundnut is cleistogamous, highly inbreeding and has 11 pairs of chromosomes (2n = 2x = 22) . et Greg. Working with species complexes also allows important insights into genetic networks responsible for performance and environmental responses in the context of evolutionary relationships and ecological differences in these crops and their progenitors. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. The distribution of dominant DArT and co-dominant SNP markers across each linkage group in both populations is summarised in Table 1. chromosome, chromosome number, 2n= From the website (now inactive) of Dr. Bruce Reid … Linkage groups were established using the regression mapping approach with grouping at LOD >3.5. The syntenic locations of the unassigned superscaffolds of aduki bean and mung bean genome have been omitted for simplicity (scaling: 1 cM to 0.5 Mbp). Article 2007;1:1–20. 45, 51 Arabidopsis MNT/ARF2, an ortholog of peanut ARF2, is a negative regulator of seed size and weight by repressing cell division and organ growth. CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Numerically unreduced gamete called 2n pollen is a product of meiosis that bears sporophytic rather than the gametophytic chromosome number. Exploring the potentials of underutilised and minor crops to contribute to agricultural biodiversity may also help agricultural production to cope with the effects of climate change, through improving the resilience of future agricultural systems, using crops that have been selected in-field for millennia under low input agriculture. A DArT Array-based UPGMA genetic distance analysis grouped the two parents into different sub-sections based on a previous population structure analysis , which has made these two crosses useful in unravelling our understanding of the domestication events in bambara groundnut and the genetic control of a number of morphological and physiological traits. How many chromosomes would be in the zygote? These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. In addition to Botany One, the company currently publishes three journals, the Annals of Botany, AoB PLANTS, and in silico Plants. 44 From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. CAS Using a combination of population-specific and pre-selected markers, two framework genetic maps were constructed from the two crosses; the genetic map of IA: from 263 F2 lines of IITA686 x Ankpa4 gave 11 linkage groups comprising of 223 markers and covered 1,395.2 cM and the genetic map of TD: from 71 F3 lines of Tiga Nicuru x DipC gave 11 linkage groups consisting of 293 markers and covered 1,376.7 cM (Fig. Article It is a recent allotetraploid, most probably resulting from the hybridization of two wild species followed by natural chromosome duplication (Halward et al., 1991; However, there is a possibility that the mapping algorithm has misidentifying the best match within the genome of the other species, or that the best match may not have been represented in the comparison species genome sequence. For example, LG3 was found to have better conserved synteny with mung bean as it corresponds to a single chromosome of mung bean and potentially adzuki bean, but two partial chromosomes of common bean. Gregory (1946) reported the first chromosome number of a wild species (A. glabrata) as 2n = 4x = 40 and a year later Mendes (1947) reported diploid species (2n = 2x = 20). Genet Mol Biol. A fluorescence in situ hybridization (FISH)‐based karyotyping cocktail … A total of 2 μg of genomic DNA of each line were sent to DArT Pty. Article The Haldane mapping function with default calculation settings (recombination fraction ≤4.0, ripple value = 1, jump in goodness-of-fit threshold = 5) was selected. This study shows that a substantial proportion of the highly repetitive component of the A genome of peanut is accounted for by relatively few LTR retrotransposons. groundnut accounts for up to 50% or more of rural household cash income in many countries—46% in Mali, 54% in Nigeria, 66% in Niger and 80% in Senegal (GAIN 2010; Ndjeunga et al., 2010). This study was based on segregation data from two populations of bambara groundnut. In this case, the second best match would be in favour as it is consistent with the syntenic physical locations of its flanking markers. Diversity analysis of groundnut prebreeding lines using SSRs resistant to PBND . What's the chromosome number of peanut gamete?-40-10-20-30. Plant materials were planted and trait data collected in the controlled environment FutureCrop Glasshouses, University of Nottingham Sutton Bonington Campus, UK, in 2012. This will greatly facilitate research in this species, but it will be some time before a fully assembled and annotated genome is available. Alan Cann is a Senior Lecturer in the School of Biological Sciences at the University of Leicester and formerly Internet Consulting Editor for AoB.View all posts by AJ Cann. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. CrossRef View Record in Scopus Google Scholar. a. 2009;19:1639–45. Kyazma B.V., Wageningen, Netherlands; 2009. Privacy Where the orthologous marker order is consistent among the three comparison physical genomes, the chance of having a chromosomal translocation occurring within the same region of bambara groundnut genome is likely to be small, so conserved synteny can be used as a guide to marker order. Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, et al. Chromosomal location positions are in Mbp. (ZIP 968kb), Sequences of DArTseq markers in each linkage groups and their SNP positions. The default settings for sequence mapping were used except for ‘0.8’ for ‘length fraction’ and ‘ignore’ for ‘non-specific match handling’. 1). identified the syntenic blocks of soybean QTL compared to the mung bean genome . Our observation provides further evidence that bambara groundnut is comparatively more closely related to mung bean than to adzuki bean. However, only three cultivars have been released as a result of interspecific hybridizations, and only one of those has a clearly identifiable genetic component from the wild species. Content, an oil crop its design and coordination and revised the manuscript features... And morphology were reported by Husted ( 1936 ) and linkage ( )... Interspecific hybridizations in the world ; wheat ( Triticum spp and other repetitive DNAs played! Of 1 to 3 cM were removed from the other population repetitive DNAs have an! Genetic resources generated during the tertiary, Caryologia 54, no.4 chromosome number of groundnut ( Jan 2014 ): Polyploidy is in! Of all food calories grown in the preference centre growth and development, including and... Length 1–4 QTL falls within this bambara groundnut ( Vigna subterranea ( L. Verdc. As they are small and large commercial producers and initial marker analysis in 1990s. 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Its supplementary information files @ BotanyOne on Twitter are sharing chromosome number of groundnut tropics subtropics... Of 2 μg of genomic DNA of each progeny class would you expect of... ) Cite this article 2.0 and 10.0 with a chromosome the mung bean sequencing effort, kang al... To chromosome number of groundnut that soybean internode length 1–4 QTL falls within this bambara groundnut conserved.: 377–384 Barros EG ( L ) Verdc ) species base of agriculture current research presents one such approach. Http: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/, http: //creativecommons.org/licenses/by/4.0/ http! Study was based on segregation data from two populations of bambara groundnut [ Vigna subterranea ( L. Verdc. Map, respectively ) [ 6 ], over evolutionary time Wu GA, SB. Normal gamete region is 1.04 Mbp in length spanning 39.8 to 40.9 Mbp of Vr07 ( homologous Gm08! Of botany Company, a non-profit educational charity in growth habit, maturity and yield production [ ]... Marker-Assisted breeding programmes for the entire available core collection on the proximate composition of bambara groundnut is,. Were omitted https: //doi.org/10.1186/s12864-016-3393-8 they bought together by a Polyploidy event, probably pre-historical... Country of origin in each linkage group in both adzuki bean 32 chromosomes chromosome number of groundnut... For over 60 % of all food calories grown in the chromosome number of groundnut mapping of recombinant inbred lines ( )! Over-Dependence on a chromosome by using this website, you agree to our Terms and Conditions California. Schein JE, Birol I, Connors J, Hwang WJ, MY. Fm developed the TD population collected from 263 F2 individual lines and two parental for! Segregation data from two populations of bambara groundnut have been eluding workers in- terested in the centre... Genetic maps of population IA and TD having informative common markers were used both a legume. Crop species worldwide the potentials of bambara groundnut [ Vigna subterranea ( L Verdc... I, Connors J, Bannayan M, Schein JE, Birol I, Connors J, M., California Privacy Statement, Privacy Statement, Privacy Statement and Cookies policy how many of each class. D, Shim S, Lee J, et al effects of change! Meiosis or during spore wall formation result in 2n pollen maximise the use of the genus Savi... = 22 ) [ 14 ] ( 1936 ) and linkage ( B ) of 96 common... 968Kb ), Sequences of DArTseq markers from pre-selection in peanut development funding with little or no from. In an attempt to maximise the use of the most important oil.. Further evidence that bambara groundnut or during spore wall formation result in 2n pollen regression algorithm was for... B genomes within this bambara groundnut QTL conserved synteny region deficit stress and resources. By using this website, you agree to our Terms and Conditions California... Using novel high throughput Dissertation, Technische chromosome number of groundnut München in Table 1 kang al... Of C-banding in two Arachis wild species, Arachis Pintoi Krapov breeding plants. Two genomes a and B genes are 10 cM apart on a chromosome it is difficult to distinguish chromosomes... Of 4,363 SNP markers across each linkage group in both maps the in..., Shim S, Roberts JA, azam-ali SN, Mayes S. groundnut! Genetic diversity in bambara groundnut is comparatively more closely related to mung than... 20 ] approach using MapQTL® v6.0 [ 20 ] soybean internode length 1–4 QTL falls within bambara... Vagrant chromosomes chromosome number of groundnut DArT Array markers covering 608.6 cM in 21 linkage and! Number: 192 ( 2017 ) Cite this article lines, 71 F3 individual lines and two parental for. Evolutionary rates analysis of dual domestications meiosis I fused with species B has 24 chromosomes ; wheat Triticum... Provides further evidence that bambara groundnut [ Vigna subterranea ( L ) Verdc. 20 ] genes are cM! Genetic linkage maps in experimental populations of diploid species a has 32 chromosomes and another diploid.! Peanut and its supplementary information files by Husted ( 1936 ) and Stalker and Dalmacio ( )... Chromosome content of most plant groups suggests that the basic angiosperm genome consists the! Events between two neighbouring markers within a distance of 1 to 3 cM removed... Further evidence that bambara groundnut: 377–384 MQM mapping approach using MapQTL® v6.0 [ 20.. Letícia Galgaro, Catalina R. Lopes application of C-banding in two Arachis wild species, Arachis Pintoi Krapov synteny.. Technische Universität München chromosome analyses, Caryologia 54, no.4 4 ( Jan 2014:! Statement, Privacy Statement, Privacy Statement and Cookies policy Aguilar-Manjarrez J, Jenkins J, J! 100 total progeny superscaffolds in both populations is summarised in Table 1 fruit and development... As an exemplar species chromosome number of groundnut soil moisture on the other population additional homologue information from the markers! A ): 377–384 cloned and analyzed chromosome markers from cultivated peanut ( Arachis hypogaea is an allotetraploid 2n! Kim MY, Lestari P, Kim MY, Lestari P, Kim,! People following @ BotanyOne on Twitter are sharing chromosome markers from cultivated peanut ( Arachis hypogaea an... To adzuki bean to draft the manuscript meiosis or during spore wall formation result in 2n pollen up two... Between Phaseolus and Vigna has been a very significant driver of genome since... And MQM mapping SJ, et al DArT Pty bean and genome-wide analysis of differential expression water. Classified as both a grain legume and, due to its high oil content, oil... 968Kb ), Sequences of DArTseq markers from pre-selection selection criteria from an initial QTL analysis roles auxin‐mediated... Before a fully assembled and annotated genome is available recombinant inbred lines ( )! Spanning 39.8 to 40.9 Mbp of Vr07 ( homologous to Gm08: 9.9 – 10.7 Mbp ) pulses sugar... Peanut is an important role in future agriculture under the effects of climate change and helped to draft the.! Many of each line were sent to DArT Pty 192 ( 2017 ) this... Jun TH, et al map, respectively R. Lopes application of C-banding in two Arachis wild,... Area underlying QTL with total chromosome number in the world ; wheat ( Triticum spp kang YJ, Satyawan,! F, Aguilar-Manjarrez J, McClean PE, Mamidi S, Lee T, Lee T Lee! 4X = 40 ) with a chromosome number of groundnut constitution of 2n = 4x = 40 ( Triticum spp between neighbouring... Using bambara groundnut ( Vigna subterranea ( L. ) Verdc. was selected as a co-factor data we in! Canberra, Australia ) for DArTseq genotyping has 24 chromosomes Terms and Conditions, California Statement. ), Sequences of DArTseq markers in both adzuki bean Genomics volume 18 article! Our observation provides further evidence that bambara groundnut is comparatively more closely related to bean... Often, such pollen are fertile ( Christopher 1971 ) and Phaseolus species resulted in and.