Genetic mapping in pea. 1. RAPD-based genetic linkage map of Pisum sativum

 A genetic linkage map of Pisum sativum L. was constructed based primarily on RAPD markers that were carefully selected for their reproducibility and scored in a population of 139 recombinant inbred lines (RILs). The mapping population was derived from a cross between a protein-rich dry-seed cultivar ‘Térèse’ and an increased branching mutant (K586) obtained from the pea cultivar ‘Torsdag’. The map currently comprises nine linkage groups with two groups comprising only 6 markers (n=7 in pea) and covers 1139 cM. This RAPD-based map has been aligned with the map based on the (JI281×JI399) RILs population that currently includes 355 markers in seven linkage groups covering 1881 cM. The difference in map lengths is discussed. For this alignment 7 RFLPs, 23 RAPD markers, the morphological marker le and the PCR marker corresponding to the gene Uni were used as common markers and scored in both populations. Received: 13 March 1998 / Accepted: 29 April 1998     

Construction of a combined sorghum linkage map from two recombinant inbred populations using AFLP,SSR, RFLP,and RAPD markers,and comparison with other sorghum maps

Sorghum [Sorghum bicolor (L.) Moench] is an important crop in the semi-arid tropics that also receives growing attention in genetic research. A comprehensive reference map of the sorghum genome would be an essential research tool. Here, a combined sorghum linkage map from two recombinant inbred populations was constructed using AFLP, SSR, RFLP and RAPD markers. The map was aligned with other published sorghum maps which are briefly reviewed. The two recombinant inbred populations (RIPs) analyzed in this study consisted of 225 (RIP 1) and 226 (RIP 2) F_3:5 lines, developed from the crosses IS 9830 2 E 36-1 (RIP 1) and N 13 2 E 36-1 (RIP 2), respectively. The genetic map of RIP 1 had a total length of 1,265 cM (Haldane), with 187 markers (125 AFLPs, 45 SSRs, 14 RFLPs, 3 RAPDs) distributed over ten linkage groups. The map of RIP 2 spanned 1,410 cM and contained 228 markers (158 AFLPs, 54 SSRs, 16 RFLPs) in 12 linkage groups. The combined map of the two RIPs contained 339 markers (249 AFLPs, 63 SSRs, 24 RFLPs, 3 RAPDs) on 11 linkage groups and had a length of 1,424 cM. It was in good agreement with other sorghum linkage maps, from which it deviated by a few apparent inversions, deletions, and additional distal regions.     

The relationship between genetic and cytogenetic maps of pea. I. Standard and translocation karyotypes.

A detailed cytogenetical study of inbred lines of pea and their F1 hybrids has been undertaken to study the relationship between the cytogenetic map and the molecular linkage map. The mitotic karyotypes of a standard pea line, JI15, a translocation line, JI61, and line JI281, a line used in the production of a mapping population, are given. A chromosome rearrangement detected by cytogenetic analysis of mitotic chromosomes has been further defined by synaptonemal complex (SC) analysis and the study of metaphase I chromosome behaviour. This meiotic analysis has allowed a comparison of SC physical lengths, observed chiasma frequencies, and recombination frequencies, as estimated from the genetic map, as a means of comparing physical and genetic distances.     

A genetic linkage map for watermelon derived from a testcross population: ( Citrullus lanatus var. citroides x C. lanatus var. lanatus) x Citrullus colocynthis

A genetic linkage map was constructed for watermelon using a testcross population [Plant Accession Griffin 14113 (Citrullus lanatus var. citroides) 2 New Hampshire Midget (NHM; C. lanatus var. lanatus)] 2 U.S. Plant Introduction (PI) 386015 (Citrullus colocynthis). The map contains 141 randomly amplified polymorphic DNA (RAPD) markers produced by 78 primers, 27 inter-simple sequence repeat (ISSR) markers produced by 17 primers, and a sequence-characterized amplified region (SCAR) marker that was previously reported as linked (1.6 cM) to race-1 Fusarium wilt [incited by Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F.Sm.) W.C. Synder &; H.N. Hans] resistance in watermelon. The map consists of 25 linkage groups. Among them are a large linkage group that contains 22 markers covering a mapping distance of 225.6 cM and six large groups each with 10-20 markers covering a mapping distance of 68.8 to 110.8 cM. There are five additional linkage groups consisting of 3-7 markers per group, each covering a mapping distance of 36.5 to 57.2 cM. The 13 remaining linkage groups are small, each consisting of 2-11 markers covering a mapping distance of 3.5-29.9 cM. The entire map covers a total distance of 1,166.2 cM with an average distance of 8.1 cM between two markers. This map is useful for the further development of markers linked to disease resistance and watermelon fruit qualities.     

Development of a mungbean ( Vigna radiata) RFLP linkage map and its comparison with lablab ( Lablab purpureus) reveals a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an inter-subspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V. radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.     

The pea early nodulin gene PsENOD7 maps in the region of linkage group I containing sym2 and leghaemoglobin

The early nodulin gene, PsENOD7, is expressed in pea root nodules induced by Rhizobium leguminosarum bv. viciae, but not in other plant organs. In situ hybridization showed that this gene is transcribed during nodule maturation in the infected cells of the proximal part of the prefixation zone II. At the transition of zone II into interzone II–III, the level of PsENOD7 mRNA drops markedly. PsENOD7 has no significant homology to other genes. RFLP mapping studies have shown that PsENOD7 is located in linkage group I between the leghaemoglobin genes and sym2.     

RFLP genetic linkage maps from four F(2.3) populations and a joinmap of Gossypium hirsutum L

An RFLP genetic linkage joinmap was constructed from four different mapping populations of cotton (Gossypium hirsutum L.). Genetic maps from two of the four populations have been previously reported. The third genetic map was constructed from 199 bulk-sampled plots of an F_2.3 (HQ95–6×’MD51ne’) population. The map comprises 83 loci mapped to 24 linkage groups with an average distance between markers of 10.0 centiMorgan (cM), covering 830.1 cM or approximately 18% of the genome. The fourth genetic map was developed from 155 bulk-sampled plots of an F_2.3 (119– 5 sub-okra×’MD51ne’) population. This map comprises 56 loci mapped to 16 linkage groups with an average distance between markers of 9.3 cM, covering 520.4 cM or approximately 11% of the cotton genome. A core of 104 cDNA probes was shared between populations, yielding 111 RFLP loci. The constructed genetic linkage joinmap from the above four populations comprises 284 loci mapped to 47 linkage groups with the average distance between markers of 5.3 cM, covering 1,502.6 cM or approximately 31% of the total recombinational length of the cotton genome. The linkage groups contained from 2 to 54 loci each and ranged in distance from 1.0 to 142.6 cM. The joinmap provided further knowledge of competitive chromosome arrangement, parental relationships, gene order, and increased the potential to map genes for the improvement of the cotton crop. This is the first genetic linkage joinmap assembled in G. hirsutum with a core of RFLP markers assayed on different genetic backgrounds of cotton populations (Acala, Delta, and Texas plain). Research is ongoing for the identification of quantitative trait loci for agronomic, physiological and fiber quality traits on these maps, and the identification of RFLP loci lineage for G. hirsutum from its diploid progenitors (the A and D genomes). Received: 23 February 2001 / Accepted: 8 June 2001     

The Potato virus S resistance gene Ns maps to potato chromosome VIII

The dominant allele Ns confers in potato resistance to Potato virus S (PVS). To identify the chromosomal location of Ns, we mapped the Ns-linked marker SCG17₄₄₈ and the ISSR marker UBC811₆₀₀ to linkage group VIII of the RFLP map of a population that did not segregate for Ns. The map position of the Ns locus on chromosome VIII was confirmed with the detection of linkage between Ns and three RFLP markers, GP126, GP189 and CP16, known to be located in a corresponding region on potato chromosome VIII. PCR-based assays were developed for these RFLP markers. The PCR primers specific for GP126 generated polymorphic products (STS marker). In the case of markers GP189 and CP16, informative polymorphism was revealed in the Ns population after digestion with the restriction enzymes HaeIII and HindIII, respectively. The genetic distance between Ns and the closest CP16 locus was 4.2 cM.     

An SSR-based genetic linkage map for perennial ryegrass (<Emphasis Type="Italic">Lolium perenne</Emphasis> L.)

A simple sequence repeat (SSR)-based linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross reference population. A total of 309 unique perennial ryegrass SSR (LPSSR) primer pairs showing efficient amplification were evaluated for genetic polymorphism, with 31% detecting segregating alleles. Ninety-three loci have been assigned to positions on seven linkage groups. The majority of the mapped loci are derived from cloned sequences containing (CA)_n-type dinucleotide SSR arrays. A small number (7%) of primer pairs amplified fragments that mapped to more than one locus. The SSR locus data has been integrated with selected data for RFLP, AFLP and other loci mapped in the same population to produce a composite map containing 258 loci. The SSR loci cover 54% of the genetic map and show significant clustering around putative centromeric regions. BLASTN and BLASTX analysis of the sequences flanking mapped SSRs indicated that a majority (84%) are derived from non-genic sequences, with a small proportion corresponding to either known repetitive DNA sequence families or predicted genes. The mapped LPSSR loci provide the basis for linkage group assignment across multiple mapping populations.     

A linkage map of the pea (Pisum sativum L.) genome containing cloned sequences of known function and expressed sequence tags (ESTs)

 A linkage map of the pea (Pisum sativum L.) genome is presented which is based on F₂ plants produced by crossing the marrowfat cultivar ‘Primo’ and the blue-pea breeding line ‘OSU442-15’. This linkage map consists of 209 markers and covers 1330 cM (Kosambi units) and includes RFLP, RAPD and AFLP markers. By mapping a number of anchor loci, the ‘Primo’בOSU442-15’ map has been related to other pea linkage maps. A feature of the map is the incorporation of 29 loci representing genes of known function, obtained from other laboratories. The map also contains RFLP loci detected using sequence-characterized cDNA clones developed in our laboratory. The putative identities of 38 of these cDNA clones were assigned by examining public-sequence databases for protein or nucleotide-sequence similarities. The conversion of sequence-characterized pea cDNAs into PCR-amplifiable and polymorphic sequence-tagged sites (STSs) was investigated using 18 pairs of primers designed for single-copy sequences. Eleven polymorphic STSs were developed. Received: 18 June 1997 / Accepted: 11 August 1997     

Cloning and mutagenesis of nodulation genes from Rhizobium leguminosarum TOM, a strain with extended host range

Summary Some primitive pea lines, e.g. cultivar Afghanistan, are resistant to nodulation by most strains of Rhizobium leguminosarum. However the Turkish strain TOM can nodulate cv. Afghanistan in addition to commercial pea varieties, and this extended host range is a property of its symbiotic plasmid, pRL5JI. A gene bank was constructed using DNA from a strain of R. leguminosarum containing pRL5JI. Following transfer to a strain of R. leguminosarum that had been cured of its symbiotic plasmid, two derivatives were isolated that contained cloned nodulation determinants, and were able to nodulate both cv. Afghanistan and a commercial pea variety. In addition, these clones conferred the ability to nodulate peas to a strain of R. phaseoli that had been previously cured of its symbiotic plasmid. One of these clones was subjected to mutagenesis with transposon Tn5, and 11 mutants were identified that were affected in nodulation ability. The sites of Tn5 insertions were mapped using restriction endonucleases and all were found to be within a region of 5 kb. The mutants fell into three classes on the basis of their map positions and their phenotypes on the two different pea lines tested. One class of mutants was affected in gene functions that were common to the nodulation of both pea hosts; a second class was impaired specifically in the nodulation of the commercial pea variety; a third class of mutant failed to confer on a normal strain of R. leguminosarum the supplementary ability to nodulate cv. Afghanistan.     

A genetic and physical map of the region containing PLASTOCHRON1, a heterochronic gene,in rice ( Oryza sativa L.)

The rice heterochronic gene plastochron1, pla1, shows shorter plastochron and ectopic expression of the vegetative program during the rice reproductive phase resulting in aberrant panicle formation. A genetic and physical map was constructed to isolate the causal gene for the pla1 syndrome. Small-scale mapping was carried out to determine the approximate map position of the pla1 locus, and then a high-resolution genetic map was made for pla1-1, one of the pla1 alleles, using an F₂ population comprising 578 pla1-1 homozygous plants. In a high-resolution genetic map, the pla1-1 locus was found to map between RFLP markers C961 and R1738A on chromosome 10, within a 3.6-cM genetic distance. A physical map encompassing the pla1-1 locus was constructed by overlapping Bacterial Artificial Chromosome (BAC) clones through chromosome walking. PCR-based RFLP markers from BAC-end clones were developed and mapped relative to the pla1 locus. Physical map construction using BAC clones indicated that a BAC clone, B44A10 (167-kb), contained the pla1 locus within 74-kb corresponding to a 0.52-cM genetic distance. Gene prediction of 74-kb region carrying the pla1 locus suggested several candidate genes for the pla1 gene. Identification of a candidate gene for pla1 will be made by sequence analysis of allele variation and cDNA screening.     

Influence of genes determining supernodulation on root colonization by the mycorrhizal fungus Glomus mosseae in Pisum sativum and Medicago truncatula mutants

Pisum sativum (pea) mutants of the wild type cv. Frisson and six supernodulating Medicago truncatula mutants of the wild-type cv. Jemalong line J5 for their ability to form endomycorrhizas. The six mutants of M. truncatula were shown to be allelic mutants of the same gene Mtsym12, whereas distinct genes (sym28 and sym29) are known to determine the supernodulation character of the P64 and P88 pea mutants, respectively. Mutant P88 of pea and the majority of the M. truncatula mutants were significantly more colonized by the mycorrhizal fungus Glomus mosseae than their corresponding wild types, 4 weeks and 30 days after inoculation, respectively. These differences were expressed essentially in transversal intensity rather than in length intensity of root colonization and appeared to correspond to an increase in arbuscule formation. Results are discussed in relation to the mutated genes and, in particular, whether the observed effects are due indirectly to plant physiological modifications or are a direct result of possible common factors of regulation of nodulation and mycorrhizal development. Accepted: 9 February 2000     

Candidate genes and QTLs for sugar and organic acid content in peach [ Prunus persica (L.) Batsch

The identification of genes involved in variation of peach fruit quality would assist breeders in creating new cultivars with improved fruit quality. Major genes and quantitative trait loci (QTLs) for physical and chemical components of fruit quality have already been detected, based on the peach [Prunus persica (L.) Batsch] cv. Ferjalou Jalousia^® (low-acid peach) 2 cv. Fantasia (normally-acid nectarine) F₂ intraspecific cross. Our aim was to associate these QTLs to structural genes using a candidate gene/QTL approach. Eighteen cDNAs encoding key proteins in soluble sugar and organic acid metabolic pathways as well as in cell expansion were isolated from peach fruit. A single-strand conformation polymorphism strategy based on specific cDNA-based primers was used to map the corresponding genes. Since no polymorphism could be detected in the Ferjalou Jalousia^® 2 Fantasia population, gene mapping was performed on the almond [Prunus amygdalus (P. dulcis)] cv. Texas 2 peach cv. Earlygold F₂ interspecific cross from which a saturated map was available. Twelve candidate genes were assigned to four linkage groups of the peach genome. In a second step, the previous QTL detection was enhanced by integrating anchor loci between the Ferjalou Jalousia^® 2 Fantasia and Texas 2 Earlygold maps and data from a third year of trait assessment on the Ferjalou Jalousia^® 2 Fantasia population. Comparative mapping allowed us to detect a candidate gene/QTL co-location. It involved a cDNA encoding a vacuolar H⁺-pyrophosphatase (PRUpe;Vp2) that energises solute accumulation, and QTLs for sucrose and soluble solid content. This preliminary result may be the first step in the future development of marker-assisted selection for peach fruit sucrose and soluble solid content.     

Mapping quantitative trait loci controlling early growth in a (longleaf pine × slash pine) × slash pine BC<Subscript>1</Subscript> family

Random amplified polymorphic DNA (RAPD) markers were employed to map the genome and quantitative trait loci controlling the early growth of a pine hybrid F₁ tree (Pinus palustris Mill. 2 P. elliottii Engl.) and a recurrent slash pine tree (P. elliottii Engl.) in a (longleaf pine 2 slash pine) 2 slash pine BC₁ family consisting of 258 progeny. Of the 150 hybrid F₁ parent-specific RAPD markers, 133 were mapped into 17 linkage groups covering a genetic distance of 1,338.2 cM. Of the 116 slash pine parent-specific RAPD markers, 83 were mapped into 19 linkage groups covering a genetic distance of 994.6 cM. A total of 11 different marker intervals were found to be significantly associated with 13 of the 20 traits on height and diameter growth using MAPMAKER/QTL. Nine of the eleven marker intervals were unique to the hybrid parent 488 genome, and two were unique to the recurrent parent 18-27 genome. The amount of phenotypic variance explained by the putative QTLs ranged from 3.6% to 11.0%. Different QTLs were detected at different ages. Two marker intervals from the hybrid parent 488 were found to have QTL by environment interactions.     

Sym2 of Pea Is Involved in a Nodulation Factor-Perception Mechanism That Controls the Infection Process in the Epidermis

In pea (Pisum sativum) up to 50 nodulation mutants are known, several of which are affected in the early steps of the symbiotic interaction with Rhizobium sp. bacteria. Here we describe the role of the sym2 gene in nodulation (Nod) factor perception. Our experiments show that the sym2A allele from the wild pea variety Afghanistan confers an arrest in infection-thread growth if the Rhizobium leguminosarum bv viciae strain does not produce Nod factors with a NodX-mediated acetylation at their reducing end. Since the induction of the early nodulin gene ENOD12 in the epidermis and the formation of a nodule primordium in the inner cortex were not affected, we conclude that more than one Nod factor-perception mechanism is active. Furthermore, we show that sym2A-mediated control of infection-thread growth was affected by the bacterial nodulation gene nodO.