Location of the self-incompatibility gene on the almond linkage map

A progeny obtained from the almond cross ‘Ferragnès’בTuono’ (Prunus amygdalus Batsch) was used to study the self-incompatibility trait in three different ways: fruit set, pollen tube growth and stylar ribonuclease activity. As expected from the genotypes of the parents, all progeny appeared phenotypically as self-compatible. However, the progeny could be scored for the segregation of stylar ribonuclease isozymes and thus allowed the incompatibility locus to be placed on the almond linkage map.     

Genetic mapping of a major gene delaying blooming time in almond

The objective of this study was to determine the genetic basis of late blooming in almond. Molecular markers were used to study the Late bloom gene (Lb), responsible for a delay of blooming time, in an F₁ segregating population of 134 plants. Using a qualitative approach, the Lb gene was located on linkage group 4 of the almond map, flanked by markers AG6 and FG3. The quantitative analysis confirmed the presence of a major gene on linkage group 4, which explained at least 79% of the phenotypic variation. On average, the plants with the Lb allele bloomed 15 days later and the Lb allele showed dominant gene action. In addition, three RAPD markers associated with the Lb gene were identified by bulked segregant analysis. One was placed at 5.4 cM from Lb and could be used as a diagnostic marker for flowering time.     

RFLP variability in apricot (Prunus armeniaca L.)

The level of polymorphism of the restriction fragment length polymorphisms (RFLPs) detected by 33 almond genomic and cDNA probes was studied in a set of 52 European and North-American apricot cultivars. Eighteen of these probes were polymorphic and yielded a total of 48 scorable bands, allowing the identification of 45 different phenotypes. Most cultivars (43) had an individually distinguishable RFLP phenotype, and three of the five clusters with the same phenotype contained cultivars that were likely to be synonymous. The group of Spanish cultivars (25) had a lower level of polymorphism than the others, suggesting that bottlenecks may have occurred in the recent history of the apricot that have eroded its genetic variability.     

Molecular markers linked to rhizomania resistance in sugar beet, Beta vulgaris, from two different sources map to the same linkage group

Rhizomania, one of the most important diseases of sugar beet, is caused by beet necrotic yellow vein virus, a Furovirus vectored by the fungus Polymyxa betae Keskin. Reduction of the production losses caused by this disease can only be achieved by using tolerant cultivars. The objective of this study was the identification and mapping of random amplified polymorphic DNA (RAPD) markers linked to a rhizomania resistance gene. The RAPD markers were identified using bulked segregant analysis in a segregating population of 62 individuals derived by intercrossing plants of the resistant commercial hybrid GOLF, and the resistance locus was positioned in a molecular marker linkage map made with a different population of 50 GOLF plants. The resistance locus, Rr1, was mapped to linkage group III of our map of Beta vulgaris L. ssp. vulgaris, which consisted of 76 RAPDs, 20 restriction fragment length polymorphisms (RFLPs), three sequence characterized amplified regions (SCARs) and one sequence tagged site (STS). In total, 101 molecular markers were mapped over 14 linkage groups which spanned 688.4 cM with an average interval length of 8.0 cM. In the combined map, Rr1 proved to be flanked by the RAPD loci RA411₁₈₀₀ and AS7₁₁₀₀ at 9.5 and 18.5cM, respectively. Moreover, in our I₂ population, we found that a set of markers shown by Barzen et al. (1997) to be linked to the ‘Holly’ type resistance gene was also linked to the ‘GOLF’-type resistance gene. These results appeared to indicate that the rhizomania resistance gene present in the GOLF hybrid could be the same gene underlying resistance in ‘Holly’-based resistant genotypes. Two other explanations could be applied: first, that two different alleles at the same locus could have been selected; second, that two different genes at two different but clustered loci underwent the selection process.     

利用2个F_2群体整合中国豌豆高密度SSR遗传连锁图谱

豌豆(Pisum sativum L.)是一种重要的食用豆类作物,在全世界范围内广泛种植,既可作为人类食物,也可作为牲畜饲料。用SSR标记构建的遗传连锁图谱在豌豆和其他作物的标记辅助育种中发挥着重要的作用。尽管对豌豆遗传连锁作图的研究已有悠久历史,但公众可获得且可转移的SSR标记以及基于遗传独特的中国豌豆种质的高密度遗传连锁图谱仍然有限。为了获得更多可转移的SSR标记和中国豌豆的高密度遗传连锁图谱,本研究首先从自主开发和文献获取的12,491个全基因组SSR标记中筛选了617个多态性SSR标记,并用于G0003973×G0005527 F_2群体遗传连锁图谱的加密。加密后的图谱全长扩展到5330.6 cM,包含603个SSR标记,标记平均间距离8.8 cM,相比之前的图谱有明显改善。基于上述结果,我们又筛选了119个具有多态性的SSR标记,用于构建大样本W6-22600×W6-15174 F_2群体的遗传连锁图谱,新图谱累积长度为1127.1 cM,包含118个SSR标记,装配在7条连锁群上。最后,将来自以上2个遗传图谱的数据进行整合,得到了一张覆盖范围6592.6 cM的整合图谱,包含668个SSR标记,由509个基因组SSR、134个EST-SSR和25个锚定标记组成,分布在7条连锁群上。这些SSR标记和遗传连锁图谱将为豌豆的遗传研究和标记辅助育种提供有力工具。     

Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F₂ mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F₂ plants were divided into three subpopulations according to the original F₁ plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, Lotus japonicus and Medicago truncatula. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.     

Genetic analysis of Lolium. I. Identification of linkage groups and the establishment of a genetic map

A genetic map of Lolium has been produced using isozyme, restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers applied to a segregating family derived from an F₁ hybrid plant of L. perenne × L. multiflorum provenance, crossed on to a doubled haploid L. perenne. A total of 106 markers, out of a total of 160 polymorphic loci analysed, have been ascribed to seven linkage groups covering a map distance of 692cM, Two of these groups may be allocated to chromosomes 2 and 6 of the Lolium genome. The remaining unallocated markers, the majority of which showed severe segregation distortion, could be associated into small groups of two or three markers which showed no linkage with the main groups at a LOD of 2.8 or, if associated, could not be mapped in a satisfactory manner. This high incidence of disturbed segregations could be accounted for by the use of an interspecific hybrid between two species of differing genome size, with consequent cytological imbalance.     

Clustering of amplified fragment length polymorphism markers in a linkage map of rye

Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI‐MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F₂ mapping population. Seventy‐one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM.     

Genetic diversity in apricot, Prunus armeniaca, aimed at improving resistance to plum pox virus

Plum Pox Virus, a non-persistent virus transmitted by aphids, causes serious damage to stone fruits. The apricot tree is very sensitive and in order to breed apricot cultivars resistant to Plum Pox Virus and establish breeding strategies, genetic diversity based on 10 enzymatic systems, six of which were polymorphic, has been studied. The plant material studied, 94 accessions, included the most important apricot cultivars grown in PPV-affected areas. Genetic diversity is high and showed important differences between the three geographical groups studied (North African, European and North American). The North American group was very diverse and allozymes can be used to identify three subgroups. Some North American PPV-resistant cultivars were very distant from the rest of the cultivars, mainly due to the presence of rare alleles found in an Asian apricot related species. These results support the hypothesis that Asian-related species might be the origin of PPV resistance within the North American cultivars. Three North American cultivars have been considered as putative donors of PPV resistance to the European cultivars because of their agronomic behaviour, chilling requirements and distance from European cultivars. However, to increase the genetic variability of the European group and thereby to favour recombination, the study of Asian apricot resources is also recommended.     

Density enhancement of a faba bean genetic linkage map (Vicia faba) based on simple sequence repeats markers

Genetic mapping for faba bean lags far behind other major crops. Density enhancement of the faba bean genetic linkage map was carried out by screening 5,325 genomic SSR primers and 2033 expressed sequence tag (EST)‐SSR primers on the parental cultivars '91825' and 'K1563'. Two hundred and fifteen genomic SSR and 133 EST‐SSR primer pairs that detected polymorphisms in the parents were used to screen 129 F₂ individuals. This study added 337 more SSR markers and extended the previous linkage map by 2928.45 cM to a total of 4516.75 cM. The number of SSR markers in the linkage groups varied from 12 to 136 while the length of each linkage group ranged from 129.35 to 1180.21 cM. The average distance between adjacent loci in the enhanced genetic linkage map was 9.71 cM, which is 2.79 cM shorter than the first linkage map of faba bean. The density‐enhanced genetic map of faba bean will be useful for marker‐assisted selection and breeding in this important legume crop.     

The ‘European Apple Genome Mapping Project’-developing a strategy for mapping genes coding for agronomic characters in tree species

Summary A recently initiated collaborative project involving apple breeders in seven European countries is described. The objective is to improve the European apple crop by molecular-aided breeding to increase efficency and reduce the time-scale in breeding for resistance, tree habit and fruit quality. The strategy adopted provides a model for similar studies in fruit, forest and other woody species. The project is based on progenies from a small number of crosses involving many important agronomic genes. Replication of these reference progenies by vegetative propagation will enable studies to be carried out simultaneously in each country. By developing a range of molecular markers, including isozymes, RFLPs and sequence-tagged DNA probes, an integrated molecular map is being constructed for use in a wide range of breeding and genetic studies. Construction of a database recording many mapped molecular markers will enable efficient exploitation of data in future genetic, breeding and physiological studies of apple. Aspects of the adopted strategy, techniques and management are discussed in the context of mapping genes in perennial crop genomes.     

Inheritance of nut and kernel traits in almond (Prunus amygdalus Batsch)

Summary An almond breeding program was initiated in 1966 to develop improved cultivars for arid conditions with irrigation. Nut and kernel traits were evaluated for almond parents and progenies. Highly significant parent/progeny correlation coefficients (0.7–0.9) were found for shell hardness, percentage of kernel, in-shell (nut) and kernel weight, kernel length and width, as well as kernel color and outer shell retention.Double kernels and kernel thickness had low parent/progeny correlation coefficients. Shell hardness and percent kernel were highly correlated, as were shell hardness and outer shell retention, percent kernel and outer shell retention, and kernel width and nut weight.All but two of the evaluated traits (kernel thickness and percent doubles) appear to be highly heritable with mostly additive gene action, although some degree of dominance appeared to be involved in percent kernel, shell hardness and percent doubles.Contribution No. 185-E from Agricultural Research Organization, Israel.     

A genetic linkage map of rhodesgrass based on an F1 pseudo-testcross population

The linkage relationships between 164 polymorphic amplified fragment length polymorphism (AFLP) and 25 restriction fragment length polymorphism (RFLP) fragments assayed in a pseudo‐testcross population generated from the mating of single genotypes from two divergent cultivars were used to construct female, ‘Katambora’ (‘Kat’) and male, ‘Tochirakukei’ (‘Toch’) parental genetic maps for rhodesgrass. The ‘Kat’ genetic map consists of 84 marker loci (72 AFLP and 12 RFLP markers) distributed on 14 linkage groups and spans a total length of 488.3 cM, with an average distance of 7.8 cM between adjacent markers. The ‘Toch’ genetic map consists of 61 marker loci (52 AFLP and nine RFLP) mapped on 12 linkage groups spanning a total length of 443.3 cM, with an average spacing of 9.0 cM between adjacent markers. About 23% of the markers remained unassigned. The level of segregation distortion observed in this cross was 11.1%. In both maps, linked duplicated RFLP loci were found. These linkage maps will serve as a starting point for linkage studies in rhodesgrass with potential application for marker‐assisted selection in breeding programmes.     

Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing

Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world’s most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between ‘Purple Sweet Lord’ (PSL) and ‘90IDN-47’ cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.     

园艺植物遗传图谱的研究进展

遗传图谱的构建是基因组研究中的重要环节,是基因定位与克隆、分子标记辅助育种的基础。对遗传图谱的构建步骤、分子标记的种类、作图群体的种类及目前国内外园艺植物遗传图谱的研究进展进行简要概述,探讨了目前该领域研究中存在的主要问题及今后的研究方向。     

Genetic and linkage analysis of isozyme loci in Daucus carota L.

Summary Electrophoretic polymorphisms of eight enzyme systems were studied in leaves of Daucus carota ssp. sativus in order to identify additional isozyme loci and generate first linkage groups of genetic markers. The genetic analysis of aconitase (ACO), leucin aminopeptidase (LAP), menadione reductase (MDR), phosphoglucomutase (PGM), 6-phosphogluconic dehydrogenase (6-PGD), shikimate dehydrogenase (SKD), and triose phosphate isomerase (TPI) zymograms resulted in the identification of 8 isozyme marker loci, designated as Aco-1, Lap-1, Pgm-1, Pgm-3, 6-Pgd-2, Skd-1, Tpi-1, and Tpi-2. All loci segregated with codominant alleles and encoded for monomers (ACO, LAP, PGM, SKD), and dimers (6-PGD, TPI), respectively. MDR enzymes of the variable region MDR-2 appeared to be identical with Dia-2 isozymes. Tests of joint segregation for pairwise comparisons of all 14 isozyme marker loci now available in carrots indicate that 12 loci are linked in 4 linkage groups (marked K1 to K4) in the following order: Aco-1, Pgi-1, and Dia-3 (K1), Tpi-2, Got-2, and Lap-1 (K2), Got-3 and Tpi-1 (K3) and Pgm-1, Pgm-3, 6-Pgd-2 and Skd-1 (K4). Dia-2 and Got-1 remained unlinked. The possible duplication of a PGM locus and a 6-PGD locus is discussed.     

AFLP fingerprinting in Medicago spp.: Its development and application in linkage mapping

Cultivated alfalfa (Medicago sativa L., 2n= 4x= 32) is one of the most important forage crops in temperate climates. The genus Medicago includes diploid species that are a valuable source of wild germplasm for studying the reproductive system of alfalfa and its abnormalities. A linkage map of an apomeiotic mutant of Medicago falcata (L.) Arcang. (2n= 2x= 16) that spanned 368.6 cM and included 29 amplified fragment length polymorphism (AFLP), 35 random amplified polymorphic DNA (RAPD) and three restriction fragment length polymorphism (RFLP) loci was constructed using a one-way pseudo-testcross mapping strategy. The success of such a strategy depends on the presence of sufficiently high levels of heterozygosity in the individual plant which is being mapped and on the informativeness of the marker system that is used. In general: (1) highly informative and reproducible RAPD and AFLP fingerprints were generated and several genome-specific primers selected; (2) of 67 marker loci mapped, 51 were arranged in 11 main linkage groups and eight additional couples of linked marker loci were detected; (3) mapping of an F₁ population theoretically allowed a better estimation of linkage distances since it avoided segregation distortion (x² analyses revealed segregation distortion in only 5.2% of marker loci); (4) the high frequency of unlinked marker loci obtained suggests that, in this alfalfa genotype, DNA markers are distributed throughout the genome. This type of genetic map should find application and prove useful in marker-assisted selection and map-based breeding programmes in meiotic mutants of alfalfa for which there is a lack of suitable genetic markers.     

Construction of a chromosome-assigned,sequence-tagged linkage map for the radish,Raphanus sativus L. and QTL analysis of morphological traits

The radish displays great morphological variation but the genetic factors underlying this variability are mostly unknown. To identify quantitative trait loci (QTLs) controlling radish morphological traits, we cultivated 94 F₄ and F₅ recombinant inbred lines derived from a cross between the rat-tail radish and the Japanese radish cultivar ‘Harufuku’ inbred lines. Eight morphological traits (ovule and seed numbers per silique, plant shape, pubescence and root formation) were measured for investigation. We constructed a map composed of 322 markers with a total length of 673.6 cM. The linkage groups were assigned to the radish chromosomes using disomic rape-radish chromosome-addition lines. On the map, eight and 10 QTLs were identified in 2008 and 2009, respectively. The chromosome-linkage group correspondence, the sequence-specific markers and the QTLs detected here will provide useful information for further genetic studies and for selection during radish breeding programs.     

The construction of a linkage map of Alstroemeria aurea by AFLP markers

An AFLP based linkage map has been generated for the ornamental crop species Alstroemeria aurea. In view of the large genome size of Alstroemeria (25,000 Mb) the number of selective nucleotides for AFLP amplification was increased to EcoRI+4/MseI+4 to generate fingerprints of moderate complexity. In addition, markers were generated with the enzyme combination Sse/Mse, where Sse8387I is an8-cutter, thereby reducing AFLP template complexity. Segregation of 374AFLP polymorphisms was recorded in the F₁ of an intraspecific A. aurea cross (A002 × A003). The map consisted of 8 A002 and 10A003 linkage groups with 122 and 214 markers covering 306.3 and605.6 cM, respectively. The two maps were integrated by using the21% of the AFLP markers that were heterozygous in both parents, and31% of the markers remained unlinked. Pollen color was assigned to linkage group A002-6. The enzyme combinations EcoRI+4/MseI+4 and Sse+2/MseI+3 generated 80 and 30 clear bands per lane with 16 and 9 polymorphic markers, respectively. Twenty percent of the EcoRI+4/MseI+4 primer combinations resulted in fingerprints that were disturbed by a few excessively thick bands (55 out of 288 primer combinations). We conclude that fingerprints and markers generated with the eight-cutter enzyme Sse8387I, in combination with+2/+3 selective nucleotides (Sse+2/MseI+3) are superior toEcoRI+4/MseI+4. This revised version was published online in August 2006 with corrections to the Cover Date.