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PubMed2003

[Research progress in forest tree genetic linkage map construction and its future prospects].

The research progress in genetic linkage map construction of forest tree species both at home and abroad were reviewed in the paper. Two main problems involved in the field were discussed. One was the limitation of the number of individuals of mapping populations and the other was the random markers mostly employed by the majority of studies. These problems have resulted in crossing combination specificity in the constructed maps and the QTLs located on the basis of the maps. As a result,the QTLs discovered up to now have low credibility and poor practicability in marker-assisted selection. Therefore considering the biological characteristics of forest tree species,the selection of the most suitable genetic markers is crucial to obtain a high quality genetic linkage map, and it is both important and necessary to carry out comparative genetic mapping. Progress in the ongoing expressed sequence tag (EST) sequencing projects were summarized and EST polymorphism (ESTP), the most informative and highly conservative marker with known function,as well as the main ESTP detection techniques were elaborated. It was pointed out that ESTP markers should be integrated into the present studies of genetic linkage map construction, QTL mapping and genome comparative mapping. Finally the future prospects in the fields of genetic linkage map and QTL mapping were discussed. In China, such studies around Populus, especially in the local Populus species should make a breakthrough in the related fields.

English Abstract↗
PubMed2002

Linkage analysis of quantitative trait loci in multiple line crosses.

Simple line crosses, for example, backcross and F2, are commonly used in mapping quantitative trait loci (QTL). However, these simple crosses are rarely used alone in commercial plant breeding; rather, crosses involving multiple inbred lines or several simple crosses but connected by shared inbred lines may be common in plant breeding. Mapping QTL using crosses of multiple lines is more relevant to plant breeding. Unfortunately, current statistical methods and computer programs of QTL mapping are all designed for simple line crosses or multiple line crosses but under a regular mating system. It is not straightforward to extend the existing methods to handle multiple line crosses under irregular and complicated mating designs. The major hurdle comes from irregular inbreeding, multiple generations, and multiple alleles. In this study, we develop a Bayesian method implemented via the Markov chain Monte Carlo (MCMC) algorithm for mapping QTL using complicated multiple line crosses. With the MCMC algorithm, we are able to draw a complete path of the gene flow from founder alleles to their descendents via a recursive process. This has greatly simplified the problem caused by irregular mating and inbreeding in the mapping population. Adopting the reversible jump MCMC algorithm, we are able to simultaneously search for multiple QTL along the genome. We can even infer the posterior distribution of the number of QTL, one of the most important parameters in QTL study. Application of the new MCMC based QTL mapping procedure is demonstrated using two different mating designs. Design I involves two inbred lines and their derived F1, F2, and BC populations. Design II is a half-diallel cross involving three inbred lines. The two designs appear different, but can be handled with the same robust computer program.

Algorithms↗
PubMed2002

Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil.

A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12. To map that major QTL with higher precision and certainty, a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake. Two different mapping strategies have been followed in this study. A conventional QTL mapping approach was based on individual F(2) RFLP data and the phenotypic evaluation of family means in the F(3). The second strategy employed a substitution-mapping approach. Phenotypic and marker data were obtained for 160 F(3) individuals of six highly informative families that differed in the size of donor chromosomal segments in the region of the putative QTL. QTL mapping showed that close to 80% of the variation between families was due to a single QTL, hereafter referred to as Pup1 (Phosphorus uptake 1). Pup1 was placed in a 3-cM interval flanked by markers S14025 and S13126, which is within 1 cM of the position identified in the original QTL mapping experiment. Other chromosomal regions and epistatic effects were not significant. Substitution mapping revealed that Pup1 co-segregated with marker S13126 and that the flanking markers, S14025 and S13752, were outside the interval containing Pup1. The two mapping strategies therefore yielded almost identical results and, in combining the advantages of both, Pup1 could be mapped with high certainty. The QTL mapping appoach showed that the phenotypic variation between families was due to only one QTL without any additional epistacic interactions, whereas the advantage of substitution mapping was to place clearly defined borders around the QTL.

Journal Article↗
PubMed2001

Localization to chicken chromosome 5 of a novel locus determining salmonellosis resistance.

Clear genetic differences in the susceptibility of chickens to visceral infection by Salmonella have been observed and it has been possible to identify resistant and susceptible lines of inbred chickens. We report here the results of experiments to map directly the gene(s) controlling this trait in chickens by examining crosses between highly susceptible and highly resistant lines. In the mapping panel, a region on chicken Chromosome (Chr) 5 was found to have a large effect on resistance, and this effect was observed in three separate resource populations. Mapping of additional marker loci in the region of the resistance gene further localized it to a region of approximately 2 cM, close to the genes for creatine kinase (CKB) and dynein (DNCH1). This region shows conserved synteny with telomeric regions of human Chr 14 and mouse Chr 12. On the basis of this conserved synteny, this resistance gene seems unlikely to correspond to the previously identified salmonellosis resistance genes Lps (located on mouse Chr 4) or Nos(2) (located on mouse Chr 11). There was no association between Nramp1 and resistance in these crosses, although this gene was shown to contribute to resistance in other crosses. The homologous human and mouse regions at present contain no likely candidate genes for this trait. Thus this appears to be a novel resistance gene, which we designate SAL1.

Animals↗
PubMed2001

Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9.

Comparative mapping of chicken and human genomes is described, primarily of regions corresponding to human chromosomes 1, 4 and 9. Segments of chicken orthologues of selected human genes were amplified from parental DNA of the East Lansing backcross reference mapping population, and the two parental alleles were sequenced. In about 80% of the genes tested, sequence polymorphism was identified between reference population parental DNAs. The polymorphism was used to design allele-specific primers with which to genotype the backcross panel and place genes on the chicken linkage map. Thirty-seven genes were mapped which confirmed the surprisingly high level of conserved synteny between orthologous chicken and human genes. In several cases the order of genes in conserved syntenic groups differs between the two genomes, suggesting that there may have been more frequent intrachromosomal inversions as compared with interchromosomal translocations during the separate evolution of avian and mammalian genomes.

Alleles↗
PubMed2007

Bypassing of a polygenic Microcyclus ulei resistance in rubber tree, analyzed by QTL detection.

Genetic resistance components of the Hevea brasiliensis x H. benthamiana RO 38 cultivar to Microcyclus ulei disease were investigated by inoculating isolates which succeeded in partially or completely infecting genotypes of a mapping population. Progeny of a cross between RO 38 and a susceptible cultivar was inoculated under controlled conditions with three isolates and scored for two resistance traits. Interval mapping and a nonparametric test were used to detect resistance quantitative trait loci (QTLs). Eight significant QTLs were detected, all of them inherited from the interspecific parent. Among these QTLs, only one contributed to the partial resistance against a highly pathogenic isolate, and no QTL was detected for resistance against the most pathogenic isolate. As an unexpected result, a single isolate can thus completely bypass this polygenic resistance. This complex situation, where no clear relationship can be established between number of resistance factors and qualitative vs quantitative or partial vs complete resistance, is discussed and suggestions as to the detection of new and sustainable resistance sources are proposed.

Ascomycota↗
PubMedDate not supplied

Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa.

Localizing genes that contribute to drought avoidance in a quantitative way should enable the exploitation of these genes in breeding through marker-assisted selection, and may lead to the discovery of gene identity and function. Between 110 and 176 F6 recombinant inbred lines from a mapping population derived from a cross of upland rice varieties Bala and Azucena have been evaluated for indicators of drought avoidance in sites in the Philippines and West Africa over two dry seasons. A molecular map with 102 RFLP, 34 AFLP and six microsatellite markers has been used to map (by composite interval mapping) quantitative trait loci (QTLs) for the visual scores of leaf rolling and leaf drying and leaf relative water content. QTLs were mapped for each site and across sites. A total of 17 regions were identified which contained QTLs with a LOD score greater than 3.2. For leaf rolling, Bala was the parent contributing the majority of positive alleles whilst for the other traits, Bala and Azucena contributed more evenly. Six of the 17 regions influenced more than one trait, explaining the phenotypic correlations between traits that were observed. Three QTLs appeared to be specific to the Philippines experiments. One QTL had opposing effects in the Philippines and West Africa. QTLs for relative water content were detected on chromosome 8, congruent with an osmotic adjustment QTL identified in another population. Only three of the QTLs identified here have not been reliably identified in the two other populations that have been screened for drought avoidance. By using several populations assessed for drought avoidance in different sites, the distribution and utility of QTLs for drought avoidance in rice is being elucidated.

Adaptation, Physiological↗
PubMed2002

Identification of genetic factors controlling the efficiency of Agrobacterium rhizogenes-mediated transformation in Brassica oleracea by QTL analysis.

We have identified quantitative trait loci (QTL) for transgenic and adventitious root production using an Agrobacterium rhizogenes-mediated co-transformation system in conjunction with a Brassica oleracea double haploid (DH) mapping population. Three QTL for green fluorescent protein (GFP)-fluorescent root production and four QTL for adventitious root production were identified as accounting for 26% and 32% of the genetic variation in the population, respectively. Two of the QTL regions identified were common to both transgenic and adventitious root production. Two different methods of QTL analysis were employed (marker regression and interval mapping) and with the exception of one region on linkage group O7 for transgenic root production, both techniques detected the same regions of the genome. The regions we identified to be associated with the control of transgenic root production following A. rhizogenes-mediated transformation are the first to be detected using a QTL mapping approach. In addition, this is the first study to identify genetic regions that co-regulate both transgenic and adventitious root production within the constraints of an A. rhizogenes-mediated transformation process. We have identified plant genotypes that do not produce any transgenic roots that may be deficient for T-DNA integration via illegitimate recombination and that may also be potentially important for the development of homologous recombination protocols. Conversely, we have also identified plant genotypes with high rates of transgenic root production that will be critical in the development of high throughput transformation systems.

Journal Article↗
PubMed2003

Molecular phylogeny of date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia by DNA fingerprinting.

Genetic diversity among 13 different cultivars of date palm (Phoenix dactylifera L.) of Saudi Arabia was studied using random amplified polymorphic DNA (RAPD) markers. The screening of 140 RAPD primers allowed selection of 37 primers which revealed polymorphism, and the results were reproducible. All 13 genotypes were distinguishable by their unique banding patterns produced by 37 selected primers. Cluster analysis by the unweighted paired group method of arithmetic mean (UPGMA) showed two main clusters. Cluster A consisted of five cultivars (Shehel, Om-Kobar, Ajwa, Om-Hammam and Bareem) with 0.59-0.89 Nei and Li's coefficient in the similarity matrix. Cluster B consisted of seven cultivars (Rabeeha, Shishi, Nabtet Saif, Sugai, Sukkary Asfar, Sukkary Hamra and Nabtet Sultan) with a 0.66-0.85 Nei and Li's similarity range. Om-Hammam and Bareem were the two most closely related cultivars among the 13 cultivars with the highest value in the similarity matrix for Nei and Li's coefficient (0.89). Ajwa was closely related with Om-Hammam and Bareem with the second highest value in the similarity matrix (0.86). Sukkary Hamra and Nabtet Sultan were also closely related, with the third highest value in the similarity matrix (0.85). The cultivar Barny did not belong to any of the cluster groups. It was 34% genetically similar to the rest of the 12 cultivars. The average similarity among the 13 cultivars was more than 50%. As expected, most of the cultivars have a narrow genetic base. The results of the analysis can be used for the selection of possible parents to generate a mapping population. The variation detected among the closely related genotypes indicates the efficiency of RAPD markers over the morphological and isozyme markers for the identification and construction of genetic linkage maps.

Alleles↗
PubMed2002

Genetic and Sequence Analysis of Markers Tightly Linked to the Soybean mosaic virus Resistance Gene, Rsv3.

Soybean mosaic virus (SMV) is a major viral pathogen, affecting soybean [Glycine max (L.) Merr.] production worldwide. The Rsv3 gene of soybean confers resistance to three of the most virulent strains (G5-G7) of SMV. The objectives of this study were to map Rsv3 and develop polymerase chain reaction (PCR) based markers for marker-assisted selection (MAS) purposes. Disease-response data were collected from two F(2) mapping populations, L29 (Rsv3) x Lee68 (rsv3) and Tousan 140 (Rsv3) x Lee68 (rsv3). Bulk segregant analysis based on amplified fragment length polymorphism (AFLP) markers demonstrated that the Rsv3 locus maps to the soybean molecular linkage group (MLG) B2 between restriction fragment length polymorphism (RFLP) markers A519 and Mng247. These two tightly linked RFLP markers were converted to PCR-based markers to expedite MAS. Sequence analysis of the Mng247 genomic region revealed similarity to the consensus sequence of a leucine-rich repeat (LRR) characteristic of the extracellular LRR class of disease resistance genes. Results from this study will be useful in pyramiding viral resistance genes and in cloning the Rsv3 gene.

Journal Article↗
PubMed2003

QTL and epistatic interaction underlying leaf chlorophyll and H2O2 content variation in rice (Oryza sativa L.).

It is meaningful to study the genetics of the traits associated with photosynthesis such as leaf chlorophyll and H2O2 contents for high yield breeding in rice. A mapping population of 98 BC1F9 lines (backcross Inbred Lines, BIL), derived from a backcross of Nipponbare (japonica)/Kasalath(indica)//Nipponbare by the single-seed-descent methods, was employed to map quantitative trait loci (QTL) underlying such rice traits as leaf chlorophyll and H2O2 contents. Five and two QTLs were detected for leaf Chlorophyll and H2O2 content variation, respectively. Among the QTLs detected, q-Chl1 on chromosome 1 accounted for 22% variation for leaf chlorophyll content variation. The alleles from Nipponbare increased stature at the locus; On the other hand, q-H2O2(1) which associated with H2O2 content was also located on the same region as q-Chl1. The alleles from Nipponbare decreased stature at this locus. The 2 traits have the 2 QTL sharing the same chromosome locations, which was located between C86 and C813 on chromosome 1. Epistasis analysis showed QTL with interaction distributed on chromosome 2, 6, 11 and 12. However, no QTL interacted with q-Chl1 or q-H2O2(1) was detected. It can be deduced that alleles from Nipponbare at the region between C86 and C813 on chromosome 1 increases leaf chlorophyll content and decreases H2O2 content at the mean time with significant additive effect but little epistasis.

Chlorophyll↗
PubMed2004

A new integrated genetic linkage map of the soybean.

A total of 391 simple sequence repeat (SSR) markers designed from genomic DNA libraries, 24 derived from existing GenBank genes or ESTs, and five derived from bacterial artificial chromosome (BAC) end sequences were developed. In contrast to SSRs derived from EST sequences, those derived from genomic libraries were a superior source of polymorphic markers, given that the mean number of tandem repeats in the former was significantly less than that of the latter ( P<0.01). The 420 newly developed SSRs were mapped in one or more of five soybean mapping populations: "Minsoy" x "Noir 1", "Minsoy" x "Archer", "Archer" x "Noir 1", "Clark" x "Harosoy", and A81-356022 x PI468916. The JoinMap software package was used to combine the five maps into an integrated genetic map spanning 2,523.6 cM of Kosambi map distance across 20 linkage groups that contained 1,849 markers, including 1,015 SSRs, 709 RFLPs, 73 RAPDs, 24 classical traits, six AFLPs, ten isozymes, and 12 others. The number of new SSR markers added to each linkage group ranged from 12 to 29. In the integrated map, the ratio of SSR marker number to linkage group map distance did not differ among 18 of the 20 linkage groups; however, the SSRs were not uniformly spaced over a linkage group, clusters of SSRs with very limited recombination were frequently present. These clusters of SSRs may be indicative of gene-rich regions of soybean, as has been suggested by a number of recent studies, indicating the significant association of genes and SSRs. Development of SSR markers from map-referenced BAC clones was a very effective means of targeting markers to marker-scarce positions in the genome.

Chromosome Mapping↗
PubMed2006

A framework linkage map of bermudagrass (Cynodon dactylon x transvaalensis) based on single-dose restriction fragments.

This study describes the first detailed linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), based on single-dose restriction fragments (SDRFs). The mapping population consisted of 113 F1 progeny of a cross between the two parents. Loci were generated using 179 bermudagrass genomic clones and 50 heterologous cDNAs from Pennisetum and rice. The map of T89 is based on 155 SDRFs and 17 double-dose restriction fragments on 35 linkage groups, with an average marker spacing of 15.3 cM. The map of T574 is based on 77 SDRF loci on 18 linkage groups with an average marker spacing of 16.5 cM. About 16 T89 linkage groups were arranged into four complete and eight into four incomplete homologous sets, while 15 T574 linkage groups were arranged into seven complete homologous sets, all on the basis of multi-locus probes and repulsion linkages. Eleven T89 and three T574 linkage groups remain unassigned. In each parent consensus maps were built based on alignments of homologous linkage groups. Four ancestral chromosomes were inferred after aligning T89 and T574 parental consensus maps using multi-locus probes. The inferred ancestral marker orders were used in comparisons to a detailed Sorghum linkage map using 40 common probes, and to the rice genome sequence using 98 significant BLAST hits, to find regions of colinearity. Using these maps we have estimated the recombinational length of the T89 and T574 genomes at 3,012 and 1,569 cM, respectively, which are 61 and 62% covered by our maps.

Chromosome Mapping↗
PubMed2005

Sugar beet BAC library construction and assembly of a contig spanning Rf1, a restorer-of-fertility gene for Owen cytoplasmic male sterility.

Rf1 is a nuclear gene that controls fertility restoration in cases of cytoplasmic male sterility caused by the Owen cytoplasm in sugar beet. In order to isolate the gene by positional cloning, a BAC library was constructed from a restorer line, NK198, with the genotype Rf1Rf1. The library contained 32,180 clones with an average insert size of 97.8 kb, providing 3.4 genome equivalents. Five AFLP markers closely linked to Rf1 were used to screen the library. As a result, we identified eight different BAC clones that were clustered into two contigs. The gap between the two contigs was filled by chromosome walking. To map the Rf1 region in more detail, we developed five cleaved amplified polymorphic sequence (CAPS) markers from the BAC DNAs identified, and carried out genotyping of 509 plants in the mapping population with the Rf1-flanking AFLP and CAPS markers. Thirteen plants in which recombination events had occurred in the vicinity of the Rf1 locus were identified and used to map the molecular markers relative to each other and to Rf1. In this way, we were able to restrict the possible location of the Rf1 gene to a minimum of six BAC clones spanning an interval of approximately 250 kb.

Beta vulgaris↗
PubMed2001

Confirmation and fine mapping of chromosomal regions influencing peak bone mass in mice.

Bone mineral density (BMD) is determined by both environmental influences and polygenic inheritance. The extreme difficulty of dissecting out environmental factors from genetic ones in humans has motivated the investigation of animal models. Previously, we used quantitative trait locus (QTL) analysis to examine peak BMD in 24 recombinant inbred (RI) mouse strains, derived from a cross between C57BL/6 (B6) and DBA/2 (D2) progenitors (RI-BXD). The distribution of BMD values among these strains indicated strong genetic influences and a number of chromosomal sites linked to BMD were identified provisionally. Using three additional independent mapping populations derived from the same progenitors, we have confirmed loci on chromosomes 1, 2, and 4, and 11 that contain genes that influence peak BMD. Using a novel fine-mapping approach (RI segregation testing [RIST]), we have substantially narrowed two of the BMD-related chromosomal regions and in the process eliminated a number of candidate genes. The homologous regions in the human genome for each of these murine QTLs have been identified in recent human genetic studies. In light of this, we believe that findings in mice should aid in the identification of specific candidate genes for study in humans.

Animals↗
PubMed2003

Chromosome mapping and identification of amphiphilic proteins of hexaploid wheat kernels.

Amphiphilic proteomic analysis was carried out on the ITMI (International Triticae Mapping Population) population resulting from a cross between "Synthetic", i.e.: "W7984" and "Opata". Out of a total of 446 spots, 170 were specific to either of the two parents, and 276 were common to both. Preliminary analysis, which was performed on 80 progenies (Amiour et al. 2002a), was completed here using a total of 101 selfed lines. Seventy two Loci of amphiphilic spots placed at LOD = 5 were conclusively assigned to 15 chromosomes. Some spots mapped during the first analysis were eliminated because of the significant distortion segregation observed in the second analysis. Group-1 chromosomes had by far the greatest number of mapped spots (51). Using the Quantitative Trait Loci (QTLs) approach, analysis of the quantitative variation of each spot revealed that 96 spots out of the 170 specific ones showed at least one Protein Quantity Locus (PQL). These PQLs were distributed throughout the genome. With Matrix Laser Desorption Ionisation Time Of Flight (MALDI-TOF) spectrometry and Database interrogation, a total of 93 specific and 41 common spots were identified. This enabled us to show that the majority of these proteins are associated with membranes and/or play a role in plant defence against external invasions. Using multiple-regression analysis, other amphiphilic proteins, in addition to puroindolines, were shown to be involved in variation in kernel hardness in the ITMI population.

Chromosome Mapping↗
PubMed2002

Molecular mapping, phenotypic expression and geographical distribution of genes determining anthocyanin pigmentation of coleoptiles in wheat ( Triticum aestivumL.).

Three major gene loci determining the anthocyanin pigmentation of coleoptiles were mapped on the short arms of chromosomes 7A, 7B and 7D, respectively. All three genes map about 15 to 20 cM distal from the centromere and, therefore, it may be concluded that they are members of a homoeologous series and should be designated Rc-A1, Rc-B1 and Rc-D1, respectively. Further homoeologous loci exist in Triticum durum, Triticum tauschii, and most probably in Secale cereale and Hordeum vulgare. By analyzing a syntheticxcultivated wheat cross (ITMI mapping population) under different environmental conditions it was shown that the expression of the genes determining anthocyanin pigmentation of the coleoptiles varies. One additional locus was detected on chromosome 4BL. Beside the mapping data, results of a screening for red coleoptile color genes in 468 mainly European wheat varieties are presented.

Journal Article↗
PubMed2003

A microsatellite marker based framework linkage map of Vitis vinifera L.

We have constructed a framework linkage map based on microsatellite markers for Vitis vinifera L., the European wine grape. The mapping population consisted of 153 progeny plants from a cross of Vitis vinifera cvs. Riesling x Cabernet Sauvignon. One hundred fifty-two microsatellite markers and one polymorphic EST marker have been mapped to 20 linkage groups (2 n=38). The map covers 1,728 cM with an average distance between markers of 11.0 cM. Estimates of genome size, expected genome coverage, and observed genome coverage were determined with 135-140 markers. Genome length estimates differed between paternal and maternal data sets. Observed approximate genome coverage was 65% versus an expected coverage of 90%. Meiotic recombination rates were not significantly different between maternal and paternal parents. This map has been adopted as a reference map for the International Grape Genome Program.

Genetic Linkage↗