Development of an SSR marker set for efficient selection for resistance to black spot disease in pear breeding

Black spot disease, which is caused by Alternaria alternata (Fries) Keissler Japanese pear pathotype, is one of the most harmful diseases in Japanese pear cultivation. Because of the potential harm of fungicides to consumers and the environment, resistant cultivars are desired. In this study, to enable efficient marker-assisted selection in pear breeding, we conducted comprehensive inoculation tests and genotyping with 207 pear cultivars. We identified a marker set (Mdo.chr11.27 and Mdo.chr11.34) suitable for selection for black spot resistance. In most susceptible cultivars, Mdo.chr11.27 amplified a 220-bp band and Mdo.chr11.34 amplified a 259-bp band. The genotype of Mdo.chr11.34 corresponds perfectly to the estimated genotype of Japanese pears susceptible to black spot disease. Using linkage analysis, we identified the positions of the gene for susceptibility to black spot disease in Chinese pear. Mdo.chr11.27 and Mdo.chr11.34 were tightly linked to susceptibility in Chinese pear, and the susceptibility gene was mapped at the top of linkage group 11, similar to that in Japanese pear. This marker set and the accumulation of phenotypic data will enable efficient marker-assisted breeding for black spot resistance in pear breeding.     

Advances in table grape breeding in Japan

In Japan, few grape cultivars related to Vitis vinifera existed 200 years ago, on account of Japan’s high rainfall. Many V. labruscana and vinifera cultivars were introduced to Japan in the 19th century. Labruscana was grown instead of vinifera, mainly because of severe disease problems and a high incidence of berry cracking. Grape breeding for table use started in the 20th century, with the goal of combining the berry quality of vinifera with the ease of cultivation of labruscana. By 1945, three strategies were used: 1) crossing among introduced diploid vinifera and vinifera-related cultivars of Japanese origin, 2) interspecific crossing in tetraploid cultivars, and 3) interspecific crossing in diploid cultivars, resulting in ‘Neo Muscat’, ‘Kyoho’, and ‘Muscat Bailey A’. Later, tetraploid interspecific crossing over generations developed many ‘Kyoho’-related cultivars, including ‘Pione’, many of which have large berries, intermediate flesh texture between the two species, a labruscan or neutral flavor, and moderate disease resistance. Interspecific diploid crossing over generations developed ‘Shine Muscat’ in 2006, with large berries, crispy flesh, a muscat flavor, no cracking, seedless fruit by gibberellin application, and moderate resistance to downy mildew and ripe rot.     

Subset selection in plant breeding practive

Summary Selection decisions in variety testing should partly be based on statistical motives. Useful tools for this are subset selection procedures. These procedures can also be used when the performed experiment has an incomplete block design or when a series of regional trials is studied. Various selection rules serve different selection goals, but they all need so-called selection constants. Often, these constants have to be approximated by computer simulation. For this simulation, and also for the execution of the selection rules, software has been developed and is available. Some practical adjustments and modifications of subset selection in plant breeding practice are proposed. Finally, a case study of selection in sugar beet is presented.     

Genomics-assisted breeding: The next-generation wheat breeding era

Common wheat provides approximately 20% of the total dietary calorie intake of human beings. Recent technological advances in whole-genome sequencing and their application in wheat and its progenitor species provide new opportunities to uncover the genetic variation of wheat traits and to accelerate the traditional breeding (TB) strategies in the context of genomics-assisted breeding (GAB). Integration of TB, marker-assisted selection (MAS) and genomic selection (GS) with high-density SNP markers is expected to accelerate the breeding process and to further enhance genetic gain. With the assistance of the next- or third-generation sequencing technologies and high-throughput phenotyping platforms, GAB can now realistically be considered in the following area: (i) genome sequencing and high-quality assembly to uncover new variations, (ii) whole-genome sequence-based association studies, (iii) gene function (or functional gene) identification and (iv) integration of whole genomic breeding information, utilizing multi-omics data and different breeding strategies. We argue that GAB is becoming the preferred strategy in pursuit of new wheat cultivars with superior traits on high yielding, high nutritional quality, climate-resilience and so on.     

Methods for evaluating fruit characters and incorporation in a final index in the Norwegian pear breeding programme

Summary In the Norwegian pear breeding programme selection is based on evaluation of 20 fruit samples together with field observations of precocity, productivity and resistance to biotic and abiotic factors. Fruit weight is recorded in grams, and then transformed to a scale of 20 gram classes. Appearance, shelf life and flavour are recorded on a 0 to 9 scale, and observations of shelf life and flavour are made at 4 defined intervals following ripening at 20 °C. The final index is made by summarizing the scores of fruit size and appearance, mean score of internal breakdown, mean score of flavour, maximum score of flavour and scores of precocity, productivity and resistance. All parameters, except mean flavour, are given a weighting of one, mean fruit flavour is given a weighting of 2. Data for 160 seedlings evaluated in 1992 is presented.     

枣树不同品种缩果病抗性与相关酶活性关系的研究

为了明确枣树不同品种缩果病抗性与保护酶活性的关系,进而为早期鉴别抗性枣树品种提供参考依据,在枣果生长时期内,定期采集田间对缩果病抗性不同枣树品种果实,测定并比较其超氧化物歧化酶(SOD)、过氧化氢酶(CAT)、过氧化物酶(POD)、苯丙氨基解氨酶(PAL)活性。结果表明,不同抗性枣树品种果实中保护酶的活性差异明显。枣果生长初期,POD活性大小与品种抗性呈现一定的负相关性,但随着果实生长,抗病品种POD活性增幅多高于感病品种;在8月枣果生长关键时期,SOD、PAL活性大小与品种抗性呈正相关,且抗病品种的SOD活性上升早于感病品种;同一时期不同品种CAT活性存在差异,但无一定规律可循。枣果发育不同时期POD、SOD和PAL 3种酶活性大小与果实抗病性存在一定的规律性关系,可作为鉴别抗病品种的生理参考指标。     

Present and future of quantitative trait locus analysis in plant breeding

The joint analysis of genotype marker segregation and phenotypic values of individuals or lines enables the detection and location of loci affecting quantitative traits (QTL). The availability of DNA markers and powerful biometric methods has led to considerable progress in QTL mapping in plants. The most obvious applications of QTL analysis seem to be marker‐assisted selection (MAS) in breeding and pre‐breeding and QTL cloning. However, other areas are envisaged where QTL analysis can contribute decisively. These are: the understanding of complex traits such as plant‐pathogen interaction; plant genomics, connecting proteins and regulatory elements of known functions to QTL by candidate gene analysis; and germplasm enhancement through a characterization that allows its efficient utilization. The success in all these applications depends primarily on the reliability and accuracy of the QTL analysis itself. Therefore, the discussion of its limitations will constitute an important part of this review.     

Comparison of a modified assay method for the endopeptidase marker Ep-D1b with the Sequence Tag Site marker XustSSR2001–7DL for strawbreaker foot rot resistance in wheat

The endopeptidase marker Ep‐D1b and Sequence Tag Site (STS) marker XustSSR2001–7DL were reported to be closely associated with the most effective resistance gene (Pch1) in wheat (Triticum aestivum L.) for strawbreaker foot rot [Pseudocercosporella herpotrichoides (Fron) Deighton]. Our objectives were to: (i) develop an efficient assay method for Ep‐D1b in wheat; (ii) correlate endopeptidase zymograms to strawbreaker foot rot reactions of various wheat genotypes; and (iii) compare the utility of Ep‐D1b and XustSSR2001–7DL for predicting disease response. An improved method of assaying for the Ep‐D1b marker using roots from a single seedling was developed, which is a 2.5‐fold improvement over the previous method. Thirty‐eight wheat genotypes with known reactions to strawbreaker foot rot were analysed for Ep‐D1b and the STS marker. Six distinct endopeptidase zymograms were identified among these 38 genotypes tested, and three of these patterns were novel. The endopeptidase marker was 100% accurate for predicting strawbreaker foot rot disease response, whereas the STS marker predicted the correct phenotype with approximately 90% accuracy. The endopeptidase marker Ep‐D1b was more effective and was more economical for use in marker‐assisted selection strategies for Pch1 in our laboratory compared with the STS marker.     

Evaluation of F2 and F3 plants introgressed with QTLs for clubroot resistance in cabbage developed by using SCAR markers

Clubroot disease caused by Plasmodiophora brassicae is one of the major diseases of Brassica crops, often devastating to the cultivation of cruciferous crops in temperate regions. In a previous study (Moriguchi et al. 1999) identified three major quantitative trait loci (QTLs) for clubroot resistance, each in a separate linkage group, in a population derived from a cross between a clubroot‐susceptible inbred cabbage line, Y2A and a resistant inbred kale line, K269. In this study, the original random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were converted into sequence‐characterized amplified region (SCAR) markers to facilitate large‐scale marker‐assisted screening of clubroot resistance in cabbage breeding. Of 15 RAPD markers closely linked to the three QTLs, nine SCARs were developed as dominant markers after cloning and sequencing. In addition, two RAPD markers were converted into co‐dominant cleaved amplified polymorphic sequence (CAPS) markers, and one RFLP marker out of three tested was converted to a dominant SCAR marker. The effect of selection for resistance by the improved markers was evaluated in progeny plants in the F2 and F3. A total of 138 F2 plants were genotyped with nine SCARs and 121 well‐distributed makers consisting of 98 RAPD, 19 RFLP, two isozymes, and two morphological markers in order to estimate the level of resistance and the proportion of undesirable alleles from the kale in non‐target areas in each of the F2 populations. An F2 plant, YK118, had kale alleles at QTL1, QTL3 and QTL9. Three F2 plants, namely, YK107, YK25 and YK51 had kale alleles at only QTL1, QTL3 and QTL9, respectively. These F2 plants were selected for their low proportion of alleles derived from kale in non‐target regions. YK118, like the resistant kale parent, expressed very high resistance to three field isolates of Plasmodiophora brassicae, whereas the mean disease index in the F2 and F3 plants carrying only single QTLs was intermediate. The QTLs showed no differential response to the isolates. These plants with improved resistance will be useful as parental inbred lines for F1 hybrids.     

Molecular markers and their applications in wheat breeding

In recent years, considerable emphasis has been placed on the development of molecular markers to be used for a variety of objectives. This review attempts to give an account of different molecular markers—restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), sequence-tagged sites (STS), DNA amplification fingerprinting (DAF), amplified fragment length polymorphisms (AFLPs) and microsatellites (STMS)—currently available for genome mapping and for tagging different traits in wheat. Other markers, including microsatellite-primed polymerase chain reaction (MP-PCR), expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also discussed. Recent information on synteny in cereal genomes, marker-assisted selection, marker validation and their relevance to cereal breeding in general and wheat breeding in particular are also examined.     

Development and agronomic performance of common bean lines simultaneously resistant to anthracnose, angular leaf spot and rust

The common bean is affected by several pathogens that can cause severe yield losses. Here we report the introgression of resistance genes to anthracnose, angular leaf spot and rust in the 'carioca-type' bean cultivar 'Rudá'. Initially, four backcross (BC) lines were obtained using 'TO', 'AB 136', 'Ouro Negro' and 'AND 277' as donor parents. Molecular fingerprinting was used to select the lines genetically closer to the recurrent parent. The relative genetic distances between 'Rudá' and the BC lines varied between 0.0% and 1.99%. The BC lines were intercrossed and molecular markers linked to the resistance genes were used to identify the plants containing the genes of interest. These plants were selfed to obtain the F₂, F₃ and F₄ plants which were selected based on the presence of the molecular markers mentioned and resistance was confirmed in the F₄ generation by inoculation. Four F_4:7 pyramid lines with all the resistance genes showed resistance spectra equivalent to those of their respective donor parents. Yield tests showed that these lines are as productive as the best 'carioca-type' cultivars.     

Molecular markers in Brassica oilseed breeding: current status and future possibilities

As PCR techniques have developed over the last 15 years, a wealth of new DNA marker technologies have arisen which have enabled the generation of high‐density molecular maps for all the major Brassica crop species. Molecular markers have also been heavily used in analyses of genetic diversity in Brassica crops. The majority of the work utilizing molecular markers in Brassica oilseed breeding has to date been based on genetic mapping using various DNA marker systems in segregating populations generated for specific investigations of particular traits of interest. For numerous qualitative traits, traditional mapping approaches have led to the development of marker‐assisted selection strategies in oilseed Brassica breeding, and in some cases to map‐based cloning of the responsible genes. For quantitative traits, however, it has become apparent that traditional mapping of quantitative trait loci (QTL) is often not sufficient to develop effective markers for trait introgression or for identification of the genes responsible. In this case, allele‐trait association studies in non‐structured genetic populations represent an interesting new approach, provided the degree of gametic phase disequilibrium between the QTL and the marker loci is sufficient. Because Brassica species represent the closest crop plant relatives to the model plant Arabidopsis thaliana, significant progress will be achieved in the coming years through integration of candidate gene approaches in crop brassicas, using the detailed information now available for the Arabidopsis genome. Integration of information from the model plant with the increasing supply of data from physical mapping and sequencing of the diploid Brassica genomes will undoubtedly give great insight into the genetics underlying both simple and complex traits in oilseed rape. This review describes the current use of available genetic marker technologies in oilseed rape breeding and provides an outlook for use of new technologies, including single‐nucleotide polymorphism markers, candidate gene approaches and allele‐trait association studies.     

黄淮麦区Fhb1基因的育种应用

小麦赤霉病是由禾谷镰孢菌引起的一种世界性重要病害,严重威胁小麦生产安全。黄淮麦区作为我国小麦主产区,赤霉病危害日趋严重,因缺乏半冬性抗源,抗赤霉病育种进展缓慢。Fhb1基因是迄今发现的效应最大、抗性最稳定,也是被广泛应用于全球小麦赤霉病抗性育种的主效基因,但Fhb1基因在黄淮麦区尚未被广泛应用。本研究以感病品种矮抗58为轮回亲本, H35为Fhb1基因供体亲本,通过有限回交和分子标记辅助选择,同时利用双单倍体育种和传统系谱选育两种方法,培育出了一批综合性状较好、具有Fhb1基因的优良新品系,其中徐麦DH9和徐麦17252经多年鉴定均达到中抗水平。在以徐麦36和徐麦2023为杂交父本的后代品系中,含Fhb1基因的家系赤霉病平均抗性明显优于感病对照。Fhb1基因的导入显著提高了赤霉病抗性,但部分家系对赤霉病仍旧表现出高感水平,说明赤霉病抗性还受到Fhb1基因以外其他遗传因素的显著影响。本研究为Fhb1基因在黄淮麦区抗赤霉病小麦育种中的应用提供了成功的经验。     

A molecular technique for selection of self-compatible varieties of Japanese pear (Pyrus pyrifolia Nakai)

The pear cultivar ‘Osa-Nijisseiki’ (S₂S^sm ₄; sm = stylar-part mutant) has been used as a parent to breed self-compatible cultivars that produce excellent fruits. However, determination of the self-compatibility of ‘Osa-Nijisseiki’ offspring requires a lot of time, 6 years or more, by conventional cross breeding. We have designed a rapid reliable method for the identification of self-compatible varieties of ‘Osa-Nijisseiki’ offspring based on the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) with S-allele specific restriction endonucleases. By using this method, 8 self-compatible varieties were selected among 16 selections resulting from a cross between the self-compatible cultivar ‘Osa-Nijisseiki’ (S₂S^sm ₄) and the self-incompatible cultivars ‘Niitaka’ (S₃S₉), ‘Whasan’ (S₃S₅), ‘Chuwhangbae’ (S₄S₆). The S-genotypes of 16 ‘Osa-Nijisseiki’ offsprings were also determined. This revised version was published online in August 2006 with corrections to the Cover Date.     

Faba bean breeding for resistance against biotic stresses: Towards application of marker technology

Summary Faba beans are adversely affected by numerous fungal diseases leading to a steady reduction in the cultivated area in many countries. Major diseases such as Ascochyta blight (Ascochyta fabae), rust (Uromyces viciae-fabae), chocolate spot (Botrytis fabae), downy mildew (Peornospora viciae) and foot rots (Fusarium spp.) are considered to be the major constraints to the crop. Importantly, broomrape (Orobanche crenata), a very aggressive parasitic angiosperm, is the most damaging and widespread enemy along the Mediterranean basin and Northern Africa. Recent mapping studies have allowed the identification of genes and QTLs controlling resistance to some of these diseases. In case of broomrape, 3 QTLs explained more than 70% of the phenotypic variance of the trait. Concerning Ascochyta, two QTLs located in chromosomes 2 and 3 explained 45% of variation. A second population sharing the susceptible parental line also revealed two QTLs, one of them likely sharing chromosomal location and jointly contributing with a similar percentage of the total phenotypic variance. Finally, several RAPD markers linked to a gene determining hypersensitive resistance to race 1 of the rust fungus U. viciae-fabae have also been reported. The aim of this paper is to review the state of the art of gene technology for genetic improvement of faba bean against several important biotic stresses. Special emphasis is given on the application of marker technology, and Quantitative Trait Loci (QTL) analysis for Marker-Assisted Selection (MAS) in the species. Finally, the potential use of genomic tools to facilitate breeding in the species is discussed. The combined approach should expedite the future development of lines and cultivars with multiple disease resistance, one of the top priorities in faba bean research programs.     

The relations of broad nematode resistance to quality characteristics as a consequence of marker-assisted selection in potato breeding programs

Cultivating resistant varieties of potato is the most effective and environmentally sound method of protecting potato crops against pests and diseases. Potato cyst nematodes (PCN) are major nematode pests causing severe constraints in potato production worldwide. There are five pathotypes of Globodrea rostochiensis (Ro1–Ro5) and three of G. pallida Pa1–Pa3. Cultivation of potato varieties with broad nematode resistance may influence the growth of the wide spectrum of PCN pathotypes, but there is limited availability of such varieties on the market. The use of molecular markers allows for the effective selection of resistant genotypes at early stages of breeding. However, the impact of early selection for nematode resistance on the agronomic value of the final selected clones is a cause of concern for potato breeders. This study investigates the relationships between the presence of the combined resistance genes H1, Gro1-4 and GpaV_vrn, which confer resistance to the nematodes, and certain agricultural traits. Clones with broad nematode resistance conferred by the genes H1, Gro1-4 and GpaV_vrn presented yields and tuber morphology traits similar to those of the clones without identified resistance genes.     

Current status of tropical fruit breeding and genetics for three tropical fruit species cultivated in Japan: pineapple,mango, and papaya

Tropical fruit crops are predominantly produced in tropical and subtropical developing countries, but some are now grown in southern Japan. Pineapple (Ananas comosus), mango (Mangifera indica) and papaya (Carica papaya) are major tropical fruits cultivated in Japan. Modern, well-organized breeding systems have not yet been developed for most tropical fruit species. Most parts of Japan are in the temperate climate zone, but some southern areas such as the Ryukyu Islands, which stretch from Kyushu to Taiwan, are at the northern limits for tropical fruit production without artificial heating. In this review, we describe the current status of tropical fruit breeding, genetics, genomics, and biotechnology of three main tropical fruits (pineapple, mango, and papaya) that are cultivated and consumed in Japan. More than ten new elite cultivars of pineapple have been released with improved fruit quality and suitability for consumption as fresh fruit. New challenges and perspectives for obtaining high fruit quality are discussed in the context of breeding programs for pineapple.     

Rapid survey for presence of a blast resistance gene Pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene

The Pi‐ta gene in rice confers resistance to strains of the blast pathogen Magnaporthe grisea (Herbert) Borr. (anamorph Pyricularia oryza Cav.) containing the corresponding avirulence gene AVR‐Pita in a gene‐for‐gene fashion. The Pi‐ta gene is a typical nucleotide‐binding site type resistance gene. Nucleotide sequences distinguishing the resistant Pi‐ta and susceptible pi‐ta alleles were previously identified and used for developing DNA markers for a resistant Pi‐ta haplotype and three susceptible pi‐ta haplotypes. In the present study, the existence of the Pi‐ta gene in 141 rice germplasm accessions was rapidly determined using these markers, and the results were confirmed by inoculating rice germplasm with an M. grisea strain containing AVR‐Pita. The Pi‐ta gene was found in accessions from several major rice producing countries, including China, Colombia, Japan, Vietnam, the Philippines, Iran and the United States. The usefulness of DNA markers for rapid determination of the genotype of rice germplasm was thus demonstrated. The Pi‐ta gene also was found in rice cultivar known to contain the Pi‐ta² gene, although the allelic relationship of these genes remains to be determined. The presence of the Pi‐ta gene in landrace cultivars in several different geographical locations, the Philippines and Vietnam, other indica rice cultivars in China and Colombia suggest that the Pi‐ta gene may have spontaneously originated in indica rice cultivars. These results are useful for incorporating the Pi‐ta gene into advanced breeding lines by marker‐assisted selection for rice breeding programmes worldwide.