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PubMed2002

Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato ( Lycopersicon spp.) and pepper ( Capsicum spp.) genomes.

Resistance against both Potato virus Y (PVY) and Tobacco etch virus (TEV) was identified in the wild tomato relative Lycopersicon hirsutum PI247087. Analysis of the segregation ratio in F(2)/F(3) and BC(1) interspecific progenies indicated that a single recessive gene, or two very tightly linked recessive loci, are involved in resistance to both potyviruses. This locus was named pot-1. Using amplified fragment length polymorphism markers and a set of L. hirsutum introgression lines, pot-1 was mapped to the short arm of tomato chromosome 3, in the vicinity of the recessive py-1 locus for resistance to corky root rot. Because of the occurrence of phenotypically similar genes in pepper ( Capsicum spp.), the comparative genetics of resistance to potyviruses between tomato and pepper was investigated. Unlike most of the comparative genetic studies on resistance genes, pot-1 was tightly flanked by the same restriction fragment length polymorphism (RFLP) markers than the pvr2/pvr5 locus for resistance to PVY and TEV from pepper. These results may indicate that recessive resistance genes against potyviruses evolve less rapidly than the majority of the dominant genes cloned so far, and consequently may belong to a different family of resistance genes.

Journal Article↗

PubMed2002

Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection.

"Zhenshan 97" is the female parent of a number of widely used hybrids for rice production in China. However, this line is of poor quality because of a high amylose content (AC), a hard gel consistency (GC) and a low gelatinization temperature (GT), together with a chalky endosperm. It had been determined that the three traits for cooking and eating quality, AC, GC and GT, are controlled by the Waxy locus and/or the tightly linked genomic region. In this study we improved the eating and cooking quality of Zhenshan 97 by introgressing the Waxy gene region from Minghui 63 (wx-MH), a restorer line, that has medium AC, soft GC and high GT. The wx-MH fragment was transferred to Zhenshan 97B by three backcrosses and one selfing, then from Zhenshan 97B to Zhenshan 97A by a cross and a backcross. Molecular marker-assisted selection was applied in the series to select for individuals carrying wx-MH, to identify recombination between the Waxy and flanking markers, and also to recover the genetic background of the recurrent parent. According to the marker genotypes, the improved versions of Zhenshan 97B and Zhenshan 97A, or Zhenshan 97B(wx-MH) and Zhenshan 97A(wx-MH), were the same as the originals except for the Waxy region of less than 6.1 cM in length. The selected lines and their hybrids with Minghui 63, or Shanyou 63(wx-MH), showed a reduced AC and an increased GC and GT, coupled with a reduced grain opacity. Field examinations of agronomic performance revealed that Zhenshan 97B(wx-MH) and Shanyou 63(wx-MH) were essentially the same as the originals except for a significant decrease in grain weight. The simultaneous improvement of AC, GA, GT and opacity, indicated that the Waxy region had major effects on the four quality traits. The improved versions of Zhenshan 97 A and B should be immediately useful in hybrid rice production.

Amylose↗

PubMed2002

Molecular mapping of the Rf1 gene restoring pollen fertility in PET1-based F1 hybrids in sunflower (Helianthus annuus L.).

Up to now a single cytoplasmic male sterility (CMS) source, PET1, is used worldwide for hybrid breeding in sunflower. Introgression of the restorer gene Rf1, responsible for fertility restoration, into new breeding material requires tightly linked markers to perform an efficient marker-assisted selection. A survey of 520 decamer primers by bulked segregant analyses identified five RAPD markers linked to the restorer gene Rf1. In a F(2) population of 183 individuals one of the RAPD markers, OPK13_454, mapped 0.8 cM from Rf1, followed by OPY10_740 with 2 cM. Bulked segregant analyses using 48 AFLP primer combinations identified 17 polymorphisms, which could be mapped in the same linkage group as Rf1. E33M61_136, and E41M48_113 were mapped 0.3 cM and 1.6 cM from the gene, respectively. Conversion of E41M48_113 into a sequence-specific marker resulted in a monomorphic pattern. However, two of the RAPD markers, OPK13_454 and OPY10_740, were successfully converted into SCAR markers, HRG01 and HRG02, which are now available for marker-assisted selection. To investigate the utility of these SCAR markers in other cross-combinations they were tested in a set of 20 lines. Comparison of the patterns of 11 restorer and nine maintainer lines of PET1 demonstrated that the markers OPK13_454/HRG01 and HRG02 were absent in all maintainer lines but present in all restorer lines, apart from the high oleic line RHA348 and the dwarf line Gio55. In addition, restorer lines developed from the interspecific hybrids Helianthus annuus x Helianthus mollis and H. annuus x Helianthus rigidus gave the same characteristic amplification products.

Chromosome Mapping↗

PubMed2002

Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection.

Fiber is a basic raw material in the textile industry. The changes in spinning technology have in common the requirement of unique and often greater cotton fiber quality, especially strength, for processing. We used a Gossypium anomalum introgression line, 7235, characterized by good fiber quality properties, to identify molecular markers linked to fiber-strength QTLs. By the use of F(2) and F(3) populations derived from a cross between 7235 and TM-1, a genetic standard of Upland cotton, nine molecular markers, three SSRs and six RAPDs, were identified to be linked to two QTLs for fiber strength. One was a major QTL, QTL(FS1), detected both in Nanjing and Hainan, China, and the Texas College Station, USA. It was found to be associated with eight markers and explained more than 30% of the phenotypic variation. QTL(FS1) was mapped to chromosome 10. The major QTL in 7235 was identified to be transferred from an Acala 3080 cotton. The marker-assisted selection revealed that DNA markers linked to this QTL could be used in increasing the fiber strength of commercial cultivars.

Chromosome Mapping↗

PubMed2003

Reproduction and cytogenetic characterization of interspecific hybrids derived from Cucumis hystrix Chakr. x Cucumis sativus L.

Interspecific hybrids between Cucumis hystrix Chakr. (2n = 2 x = 24) and Cucumis sativus L. (2n = 2 x = 14) were produced by means of F(1) (2n = 19) embryo rescue and subsequent chromosome doubling. The hybridity was confirmed by genomic in situ hybridization (GISH) and chromosome analysis. The amphidiploid (2n = 38) was self-pollinated and backcrossed to cucumber resulting in lines with improved crossability to C. sativus. Examination of shape, stainability, and germination rate of pollen grains and yield as a function of mature fruit set per ten pollinated flowers indicated a tendency for increased fertility in BC(1)S(1) progeny when compared to F(1) and amphidiploid offspring. Cytogenetic characterization of F(1) and amphidiploid progeny was performed. Generally normal meioses produced viable pollen grains, and fertilization resulted in partial fertility restoration in amphidiploid progeny. Chromosome anomalies such as "frying-pan trivalent", chromosome lagging and spindle mis-orientation were also observed. In most of the PMCs of the F(1) diploid hybrid progeny, 19 univalents were observed at diakinesis and MI. In the amphidiploid, more than 90% of the configurations at MI consisted of the predicted 19 bivalents and less than 5% contained multivalents [trivalents (2.3%) + quadrivalents (0.3%)], suggesting the presence of preferential pairing, and a distinctive parental genome as well. The chiasmata observed between homoeologous chromosomes further demonstrated the introgression of the C. hystrix genome into that of C. sativus.

Chimera↗

PubMed2002

Development of isothiocyanate-enriched broccoli, and its enhanced ability to induce phase 2 detoxification enzymes in mammalian cells.

Broccoli florets contain low levels of 3-methylsuphinylpropyl and 4-methylsulphinylbutyl glucosinolates. Following tissue disruption, these glucosinolates are hydrolysed to the corresponding isothiocyanates (ITCs), which have been associated with anticarcinogenic activity through a number of physiological mechanisms including the induction of phase II detoxification enzymes and apoptosis. In this paper, we describe the development of ITC-enriched broccoli through the introgression of three small segments of the genome of Brassica villosa, a wild relative of broccoli, each containing a quantitative trait locus (QTL), into a broccoli genetic background, via marker-assisted selection and analysis of glucosinolates in the florets of backcross populations. Epistatic and heterotic effects of these QTLs are described. The ITC-enriched broccoli had 80-times the ability to induce quinone reductase (a standard assay of phase II induction potential) when compared to standard commercial broccoli, due both to an increase in the precursor glucosinolates and a greater conversion of these into ITCs.

Anticarcinogenic Agents↗

PubMed2002

Linkage of the A locus for the presence of anthocyanin and fs10.1, a major fruit-shape QTL in pepper.

The purple color of the foliage, flower and immature fruit of pepper ( Capsicum spp.) is a result of the accumulation of anthocyanin pigments in these tissues. The expression of anthocyanins is controlled by the incompletely dominant gene A. We have mapped A to pepper chromosome 10 in a Capsicum annuum (5226) x Capsicum chinense (PI 159234) F(2) population to a genomic region that also controls anthocyanin expression in two other Solanaceous species, tomato and potato, suggesting that variation for tissue-specific expression of anthocyanin pigments in these plants is controlled by an orthologous gene(s). We mapped an additional locus, Fc, for the purple anther filament in an F(2) population from a cross of IL 579, a C. chinense introgression line and its recurrent parent 100/63, to the same position as A, suggesting that the two loci are allelic. The two anthocyanin loci were linked to a major quantitative trait locus, fs10.1, for fruit-shape index (ratio of fruit length to fruit width), that also segregated in the F(2) populations. This finding verified the observation of Peterson in 1959 of linkage between fruit color and fruit-shape genes in a cross between round and elongated-fruited parents. The linkage relationship in pepper resembles similar linkage in potato, in which anthocyanin and tuber-shape genes were found linked to each other in a cross of round and elongated-tuber parents. It is therefore possible that the shape pattern of distinct organs such as fruit and tuber in pepper and potato is controlled by a similar gene(s).

Anthocyanins↗

PubMed2003

Development of PCR-based markers linked to dominant genes for male-fertility restoration in Pampa CMS of rye (Secale cereale L.).

Cytoplasmatic male sterility (CMS) is the basis for commercial hybrid seed production of rye. Nuclear restorer genes are indispensable for a complete restoration of fertility of the CMS lines. The drawbacks of current European restorer lines require the utilisation of new genetic resources that have been recently detected in an Iranian primitive rye population (IRAN IX) and an Argentinean landrace (Pico Gentario). The introgression of these effective restorer genes (Rfp1 and Rfp2, respectively) into breeding material can be facilitated by marker-assisted selection. Using two F(2) populations based on crosses between the non-restorer inbred line Lo6 and the restorer IRAN IX, as well as Pico Gentario, RAPDs and AFLPs were screened and led to a closely linked marker set for each of these genes. The conversion of the closest markers into fragment-specific sequence-characterised amplified region (SCAR) markers resulted in flanking ranges of 2.9 cM (Rfp1) and 5.2 cM (Rfp2). The application of these markers in backcross programmes is discussed.

Genes, Dominant↗

PubMed2003

Synthesis of intergeneric hybrids and establishment of genomic affinity between Diplotaxis catholica and crop Brassica species.

Intergeneric hybrids of the wild crucifer Diplotaxis catholica (2n = 18, D(C)D(C)) as female with two crop Brassica species, namely Brassica rapa (2n = 20; AA) and Brassica juncea (2n = 36; AABB) as male, were developed, using ovary and sequential culture. Reciprocal crosses were not successful, suggesting unilateral cross incompatibility. Morphologically, the hybrid plants resembled the crop brassica parents, but were nearly male- as well as female-sterile. Induction of amphiploidy helped to improve pollen fertility for the D. catholica x B. rapa cross (73%), but less so for the D. catholica x B. juncea cross (35-40%). Female fertility was also higher in both the amphiploids. Cytological analysis of the F(1) hybrids revealed aberrant meiosis with predominant occurrence of the univalents. Partial genomic homoeology between the A genome of B. rapa and the D(C) genome of D. catholica was indicated by the presence of up to five bivalents in 14.7% of the PMCs in the D. catholica x B. rapa hybrid, and 1-2 trivalents or a quadrivalent in nearly 44% of the PMCs in the derived amphiploid. In the second cross, D. catholica x B. juncea, up to six bivalents and one trivalent were observed indicating homoeology between the A/B genomes of B. juncea and the D(C) genome of D. catholica. The possibility of introgression of desirable genes from D. catholica into crop Brassica species exists in view of significant affinity between the D(C) and A/B genomes.

Brassica↗

PubMed2003

Leaf-rust resistance in rye (Secale cereale L.). 1. Genetic analysis and mapping of resistance genes Pr1 and Pr2.

Genetic analysis of resistance to leaf rust in rye (Puccinia recondita f. sp. secalis) led to the identification of two dominant resistance genes, Pr1 and Pr2. Both genes proved to be effective against a local leaf-rust population as well as a subset of single-pustule isolates (SPIs) the latter of which comprised SPIs with very high virulence complexity. Resistance conferred by Pr1 and Pr2 was expressed in detached-leaf tests of seedlings as well as in field tests of adult plants. Molecular marker analysis allowed us to map Pr1 in the proximal part of rye chromosome 6RL, whereas Pr2 was assigned to the distal part of chromosome 7RL. These results are discussed in view of homoeology relationships among Triticeae. A proposal is submitted for the designation of resistance genes to rye leaf rust which would avoid interference with existing gene-symboling in respect to wheat leaf-rust resistances introgressed from rye into wheat or triticale.

Basidiomycota↗

PubMed2003

Molecular differentiation and diversity among the California red oaks (Fagaceae; Quercus section Lobatae).

A recent epidemic of Phytopthora (Sudden Oak Death) in coastal woodlands of California is causing severe mortality in some oak species belonging to the red oak (Lobatae) group. To predict the risks of spread of this disease, an understanding of the relationships among California's red oak species and of their population genetic structure is needed. We focus here on relationships among the four species of red oak. Whereas morphological distinction of Quercus wislizeni and Quercus parvula can pose problems, Quercus kelloggii and Quercus agrifolia in pure forms are easily distinguishable from one another and from Q. wislizeni and Q. parvula in the field. However, hybrids among all species combinations are known to occur in nature and these can confound data from ecological studies. Our results revealed greatest differentiation of the deciduous Q. kelloggii, with only weak AFLP fragment differentiation of the three remaining evergreen species. The molecular data suggest a closer affinity of Q. agrifolia with Q. wislizeni and Q. parvula contrary to earlier suggestions that its origins are likely to have been with northern deciduous oaks probably through a common ancestor with Q. kelloggii. Interior and coastal populations of Q. wislizeni separated in dendrograms based on phenetic and genetic distances suggesting probable isolation in different glacial refugia. The position of Q. parvula remains ambiguous, having a closer affinity with interior populations of Q. wislizeni and with Q. agrifolia, than with coastal populations of Q. wislizeni. Mean population differentiation in Q. wislizeni was 0.18, which is somewhat higher than the average for other oak species, suggesting that range fragmentation has occurred in the past, resulting in a metapopulation structure. Our results provide evidence that introgression among these species may be causing reticulation, further confounding species separation. Whereas Phytopthora has been reported on Q. agrifolia, Q. parvula and Q. kelloggii, it has not yet been detected in natural populations of Q. wislizeni. The species relationships that our molecular data show suggest that this is more likely a result of escape due to ecological tolerances than to genetic differences.

California↗

PubMed2003

Biochemical and genetic studies of two Heterodera avenae resistance genes transferred from Aegilops ventricosa to wheat.

Two Heterodera avenae resistance genes, Cre2 from Aegilops ventricosa AP-1 and Cre5 from Ae. ventricosa #10, were shown to confer a high level of resistance to the Spanish pathotype Ha71. No susceptible plants were found in the F(2) progeny from the cross between the two accessions of Ae. ventricosa, suggesting that their respective resistance factors were allelic. However, genes Cre2 and Cre5 apparently were transferred to a different chromosomal location in the wheat line H-93-8 and in the 6M(v)(6D) substitution, respectively, as proved by F(2) segregation of their cross progeny. The induction of several defence responses during early infection by the same H. avenae pathotype in resistant lines carrying Cre2 or Cre5 genes was studied. Isoelectrofocusing (IEF) isozyme analysis revealed that peroxidase, esterase and superoxide dismutase activity increased after nematode infection, in roots of resistant lines in comparison with their susceptible parents. Differential induced isoforms were also identified when IEF patterns of resistant lines were compared. A DNA marker, absent in Cre5-carrying genotypes, was found to be linked, thought not very tightly, to the Cre2 gene in the H-93-8 line. The differences observed between the Cre2 and Cre5 genes with respect to their chromosomal location in wheat introgression lines, de-toxificant enzyme induction and behaviour against different pathotypes, suggest they are different H. avenae resistance sources for wheat breeding.

Animals↗

PubMed2003

QTLs for resistance to powdery mildew in pepper under natural and artificial infections.

Epidemics of powdery mildew due to Leveillula taurica is an increasing problem in pepper production areas, particularly in coastal regions or greenhouse cultivation. The highly resistant genitor 'H3' was submitted to genetic analysis and QTL mapping in order to promote the introgression of its oligogenic resistance into large and sweet-fruited cultivars. The doubled-haploid progeny from the cross 'H3' (resistant) by 'Vania' (susceptible) was tested for resistance under both natural field infection and artificial inoculation tests, and QTL detection was compared for those two methods. Seven genomic regions including additive QTLs and epistatic interactions were detected, explaining altogether the major part of genotypic variance. Two genomic regions were common to both the evaluation methods, whereas other QTLs were method-specific, reflecting the environment dependence of powdery mildew epidemics. Orthologies with tomato genomic regions carrying resistance genes to L. taurica and Oidium lycopersicum were revealed by comparative mapping with pepper. Tight linkages between the detected QTLs and virus resistance or fruit color traits in pepper were also shown, which adds to the agronomic importance of these regions in pepper breeding programs.

Ascomycota↗

PubMed2003

Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm.

It has been argued that the level of genetic diversity in the modern durum wheat ( Triticum turgidum L. var. durum) elite germplasm may have declined due to the high selection pressure applied in breeding programs. In this study, 58 accessions covering a wide spectrum of genetic diversity of the cultivated durum wheat gene pool were characterized with 70 microsatellite loci (or simple sequence repeats, SSRs). On average, SSRs detected 5.6 different allelic variants per locus, with a mean diversity index (DI) equal to 0.56, thus revealing a diversity content comparable to those previously observed with SSRs in other small-grain cereal gene pools. The mean genetic similarity value was equal to 0.44. A highly diagnostic SSR set has been identified. A high variation in allele size was detected among SSR loci, suggesting a different suitability of these loci for estimating genetic diversity. The B genome was characterized by an overall polymorphism significantly higher than that of the A genome. Genetic diversity is organised in well-distinct sub-groups identified by the corresponding foundation-genotypes. A large portion (92.7%) of the molecular variation detected within the group of 45 modern cvs was accounted for by SSR alleles tracing back to ten foundation-genotypes; among those, the most recent CIMMYT-derived founders were genetically distant from the old Mediterranean ones. On the other hand, rare alleles were abundant, suggesting that a large number of genetic introgressions contributed to the foundation of the well-diversified germplasm herein considered. The profiles of recently released varieties indicate that the level of genetic diversity present in the modern durum wheat germplasm has actually increased over time.

Alleles↗

PubMed2003

Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.

Hybridization and introgression are important natural evolutionary processes that can be successfully investigated using molecular markers and open- and controlled-pollinated progeny. In this study, we collected open-pollinated seeds from Cedrus atlantica, Cedrus libani and C. libani x C. atlantica hybrids from three French-plantation forests. We also used pollen from C. libani and Cedrus brevifolia to pollinate C. atlantica trees. The progeny were analyzed using three different types of molecular markers: RAPDs, AFLPs and cpSSRs. Chloroplast DNA was found to be paternally inherited in Cedrus from the progeny of controlled-crosses. Heteroplasmy, although possible, could not be undoubtedly detected. There was no indication of strong reproductive isolating barriers among the three Mediterranean Cedrus taxa. Gene flow between C. atlantica and C. libani accounted for 67 to 81% of viable open-pollinated seedlings in two plantation forests. We propose that Mediterranean Cedrus taxa should be considered as units of a single collective species comprising two regional groups, North Africa and the Middle East. We recommend the use of cpSSRs for monitoring gene flow between taxa in plantation forests, especially in areas where garden specimens of one species are planted in the vicinity of selected seed-stands and gene-conservation reserves of another species.

Cedrus↗

PubMed2003

Molecular markers linked to the blast resistance gene Pi-z in rice for use in marker-assisted selection.

Rice blast, caused by the fungal pathogen Pyricularia grisea, is a serious disease affecting rice-growing regions around the world. Current methods for identification of blast-resistant germplasm and progeny typically utilize phenotypic screening. However, phenotypic screens are influenced by environmental conditions and the presence of one resistance gene can sometimes phenotypically mask other genes conferring resistance to the same blast race. Pi-z is a dominant gene located on the short arm of chromosome 6 that confers complete resistance to five races of blast. Using sequence data found in public databases and degenerate primer pairs based on the P-loop, nucleotide binding sites and kinase domain motifs of previously cloned resistance genes, we have developed PCR-based DNA markers that cosegregate with the gene. These markers are polymorphic in a wide range of germplasm, including the narrow crosses characteristic of applied rice-breeding programs. They can now be used as a low cost, high-throughput alternative to conventional phenotypic screening for direct detection of blast resistance genes, allowing rapid introgression of genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more-durable blast resistance.

Chromosome Mapping↗

PubMed2003

Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon.

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC(2)F(2 )families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.

Crosses, Genetic↗

PubMed2003

Transmission and recombination of homeologous Solanum sitiens chromosomes in tomato.

The goal of the present experiments was to transfer the chromosomes of Solanum sitiens (syn. Solanum rickii) into cultivated tomato ( Lycopersicon esculentum). By crossing an allotetraploid L. esculentum x Solanum sitiens hybrid to sesquidiploid L. esculentum x S. lycopersicoides, a trigenomic hybrid (2n+14=38) was obtained. Analysis of the latter by GISH (genomic in situ hybridization) indicated it contained a full set of 12 S. sitiens chromosomes, plus two extras from S. lycopersicoides. This and other complex hybrids were pollinated with Lycopersicon pennellii-derived bridging lines to overcome unilateral incompatibility. A total of 40 progeny were recovered by embryo rescue, including diploids and aneuploids (up to 2n+8). In order to determine the origin of chromosomes and the location of introgressed segments, progeny were genotyped with RFLP markers. S. sitiens-specific markers on all chromosomes, except 6 and 11, were detected in the progeny. Several S. sitiens chromosomes were transmitted intact, either through chromosome addition (i.e., trisomics) or substitution (i.e., disomics). Recombination between S. sitiens and L. esculentum was detected on most chromosomes, in both diploid and aneuploid progeny. A monosomic alien addition line for S. sitiens chromosome 8 was identified, and the extra chromosome was stably transmitted to approximately 13% of the backcross progeny. This study demonstrates the feasibility of gene transfer from S. sitiens to L. esculentum through chromosome addition, substitution, and recombination in the progeny of complex aneuploid hybrids.

Chromosomes, Plant↗