作物驯化和品种改良所选择的关键基因及其特点

近15~20年作物基因组学迅速发展,特别是第2代测序技术的普及,显著降低了测序成本,使单核苷酸多态性(SNP)分析和单元型区段(也称单倍型区段)分析渗透到生命科学的各个领域,对系统生物学、遗传学、种质资源学和育种学影响最为深刻,使其进入基因组学的全新时代。一批驯化选择基因的克隆,特别是对一些控制复杂性状形成的遗传基础及其调控机制的解析,更清晰地揭示了作物驯化和品种改良的历史,提升了人们对育种的认知,推动育种方法的改进。驯化和育种既有相似之处,也存在明显的差异。驯化选择常常发生在少数关键基因或位点,对基因的选择几乎是一步到位;而现代作物育种虽然只有100年左右的历史,但其对基因组影响更为强烈,是一些重要代谢途径不断优化的过程。随着生态环境或栽培条件的变化,育种选择目标基因(等位变异)会发生相应的变化或调整,因此对基因(等位变异)的选择是逐步的。此外,强烈的定向选择重塑了多倍体物种的基因组,使其亚基因组与供体种基因组明显不同。在群体水平上,系统分析驯化和育种在作物基因组和基因中留下的踪迹,凝炼其中的规律,将为品种改良和育种提供科学理论和指导,本文也简要介绍了"十三五"国家重点研发计划专项"主要农作物优异种质资源形成与演化规律"的基本研究思路。     

The use of conventional and molecular genetics to produce new diversity in seed oil composition for the use of plant breeders-progress, problems and future prospects

Summary Considerable advances in the manipulation of seed oil yield and quality have been made using conventional breeding methods. Newer methods such as induced mutation and wide crosses have also resulted in significant achievements. These techniques, however, are all limited by the gene pool available in the crop of interest and its near relatives. The prospect of diminishing supplies of non-renewable fossil hydrocarbon reserves and the reality of edible crop surpluses have focused attention on the development of industrial oilseed crops. This will require the production of types of seed fatty acids which are not available in the oilseed crop species that are grown at present.The introduction of novel oil crops via domestication is contrasted with the insertion of alien genes into existing oilseeds to create designer crops. The use of molecular genetics to alter the yield and quality of rapeseed oil is discussed, and strategies for the engineering of seven new designer rapeseed varieties are presented.     

Application of in vivo and in vitro mutation techniques for crop improvement

Summary Conventional mutation techniques have often been used to improve yield, quality, disease and pest resistance in crops, or to increase the attractiveness of flowers and ornamental plants. More than 1700 mutant varieties involving 154 plant species have been officially released. In some economically important crops, e.g. barley, durum wheat and cotton, mutant varieties occupy the majority of cultivated areas in many countries. Mutation techniques have become one of the major tools in the breeding of ornamentals such as alstroemeria, begonia, chrysanthemum, carnation, dahlia and streptocarpus. The use of in vitro techniques such as anther culture, shoot organogenesis, somatic embryogenesis and protoplast fusion can overcome some of the limitations in the application of mutation techniques in both seed and vegetatively propagated crops. In vitro culture in combination with induced mutations can speed up breeding programmes, from the generation of variability, through selection, to multiplication of the desired genotypes. The expression of induced mutations in the pure homozygote obtained through microspore, anther or ovary culture, can enhance the rapid recovery of the desired traits. In some vegetatively propagated species, mutations in combination with in vitro culture technique, may be the only method of improving an existing cultivar. Currently, many molecular studies rely on the induction and identification of mutants in model species for construction and subsequent saturation of genetic maps, understanding of developmental genetics and elucidation of biochemical pathways. Once identified and isolated, the genes that encode agronomically-important features can be either introduced directly into crop plants or used as probes to search for similar genes in crop species. It seems most likely that the recent developments based on these technologies will soon provide improved methods for selection of desired mutants.     

中国作物新基因发掘：现状、挑战与展望

中国作物新基因发掘是实现中国作物种质资源优势向基因资源优势转变和作物分子育种的基础。本文对中国近10年来水稻、小麦、玉米、大豆、棉花和油菜等主要作物基因发掘研究的进展进行了分析和评述。中国作物基因发掘也取得了一系列突破性进展：(1)创制出一批具有特色的基因发掘材料,包括基于中国作物遗传多样性的核心种质、基于优异资源的遗传分离群体和基于人工诱变的突变体等;(2)基因发掘技术和方法有所突破,尤其是在针对基因特点整合各种基因发掘技术、改进基因/QTL的生物统计算法等,提高了基因发掘的效率;(3)作物农艺性状的标记与基因定位已成为常规遗传研究方法,初步定位了一批抗病、抗逆、优质、养分高效、高产相关基因/QTL,其中,有500多个基因已精细定位;(4)以水稻为代表的作物基因克隆及功能研究在国际上受到瞩目,在主要作物中已克隆了300多个基因,其中,在目标作物中验证的基因数超过70个。在国际作物基因发掘高效化、规模化及实用化发展过程中,中国作物基因发掘也取得了重要进展。然而,中国作物基因发掘的数量和质量还远远不能满足作物分子育种的需求,与国际作物基因发掘也存在差距,具体表现为不同作物基因发掘研究进展不平衡、发掘基因的数量还相对有限、已发掘的基因中具有重大利用价值的基因不多。针对中国基因发掘面临的问题和世界各国以及跨国生物技术公司争夺基因的巨大挑战,作者提出了中国作物基因发掘应重点提高基因发掘效率,加强重要基因克隆及基因的价值评估,以生物产业发展需求为导向的基因发掘策略。     

The potential of somatic hybridization in crop breeding

Summary In recent years, the rapid development of somatic cell genetics has made possible the transfer of alien genes over wide taxonomic distances by somatic hybridization. In this review, the potential of somatic hybridization in the breeding of crops within the Brassicaceae, Fabaceae, Poaceae and Solanaceae is discussed. It is evident from these studies that many hybrids, either symmetric or asymmetric, which are fertile have the potential to be used as a bridge between the alien species and the crop. Progeny analysis of some hybrid combinations also reveals intergenomic translocations which may lead to the introgression of the alien genes. Furthermore, fusion techniques enable the resynthesis of allopolyploid crops to increase their genetic variability and to restore ploidy level and heterozygosity after breeding at reduced ploidy level in polyploid crops.     

A non-invasive crop ideotype to reduce invasive potential

Summary In plant breeding programs, qualitative and quantitative traits confer market value and, thus, constitute the basis for developing breeding criteria during crop domestication. Some traits such as high male/female fertility are advantageous in the wild and could enable the evolution of cultivated crops into invasive weeds. Other traits, e.g. sterility, are not expected to confer invasiveness. To date there has been very limited involvement in invasion risk assessment by plant breeders. Thus, in this paper we propose that trait-based selection of potential crop species be coupled with species design in the creation of a “non-invasive crop ideotype” as an avenue to reduce invasiveness during domestication. The non-invasive crop ideotype embodies the ideal characteristics for a crop to excel in cultivated environment(s) but minimizes the likelihood it will establish and spread in non-cultivated environments, constituting the underlying foundation for all breeding objectives, choice(s) of breeding methodologies, and propagation techniques for non-invasive crop release. Using ornamental (floriculture) horticultural crops as an example, we identify 10 traits to be used individually or in combination to reduce invasiveness while retaining commercial value: reduced genetic variation in propagules, slowed growth rates, non-flowering, elimination of asexual propagules, lack of pollinator rewards, non-shattering seed, non-fleshy fruits, lack of seed germination, sterility, and programmed death (apotopsis). A non-invasive crop ideotype would constitute the underlying foundation for all breeding objectives, the choice(s) of breeding methodologies, and propagation technique(s). The ideotype should be flexible and should adjust to species- and crop-specific traits to account for the intended use. For example, development of sterile cultivars may have negligible effects in reducing invasiveness if the crops spread vegetatively. A non-invasive crop ideotype may increase the direct participation of plant breeders, who are the professionals directly involved in the collection, development and release of new crops, in reducing the invasive potential of ornamental crops. Future research is required to determine the feasibility of incorporating each trait into various crops, use of classical or molecular techniques for creation of non-invasive crops, trait stability (lack of genotype × environment interaction over years and locations), consumer acceptance, and long-term viability.     

Microsatellite markers: an overview of the recent progress in plants

In recent years, molecular markers have been utilized for a variety of applications including examination of genetic relationships between individuals, mapping of useful genes, construction of linkage maps, marker assisted selections and backcrosses, population genetics and phylogenetic studies. Among the available molecular markers, microsatellites or simple sequence repeats (SSRs) which are tandem repeats of one to six nucleotide long DNA motifs, have gained considerable importance in plant genetics and breeding owing to many desirable genetic attributes including hypervariability, multiallelic nature, codominant inheritance, reproducibility, relative abundance, extensive genome coverage including organellar genomes, chromosome specific location and amenability to automation and high throughput genotyping. High degree of allelic variation revealed by microsatellite markers results from variation in number of repeat-motifs at a locus caused by replication slippage and/or unequal crossing-over during meiosis. In spite of limited understanding of the functions of the SSR motifs within the plant genes, SSRs are being widely utilized in plant genome analysis. Microsatellites can be developed directly from genomic DNA libraries or from libraries enriched for specific microsatellites. Alternatively, microsatellites can also be found by searching public databases such as GenBank and EMBL or through cross-species transferability. At present, EST databases are an important source of candidate genes, as these can generate markers directly associated with a trait of interest and may be transferable in close relative genera. A large number of SSR based techniques have been developed and a quantum of literature has accumulated regarding the applicability of SSRs in plant genetics and genomics. In this review we discuss the recent developments (last 4–5 years) made in plant genetics using SSR markers.     

棉花纤维特异/优势表达基因的染色体定位

 棉纤维是研究植物细胞伸长和细胞壁建成以及纤维素生物合成的优良模型,迄今为止,已经分离了许多纤维特异/优势表达的基因。为了便于这些基因的图位克隆使其能够应用于棉花纤维品质的改良中,本研究采用分离群体定位法和Blast分析法对这些基因进行染色体定位。利用陆地棉、海岛棉BC₁种间分离群体,将GhCFE定位在第6染色体,GhGLP1-250定位在第19染色体。Blast分析将11个基因定位到棉花染色体上。这些基因与棉纤维的伸长和细胞壁的合成相关,与这些基因连锁标记的获得有助于棉花纤维长度和强度的分子标记辅助选择。     

小麦细胞分裂素氧化酶基因Tackx3参与穗粒数的形成

细胞分裂素氧化酶基因与禾本科作物的穗粒数密切相关.本文根据已报道的小麦细胞分裂素氧化酶(cytokinin oxidase,CKX)基因EST序列在GenBank中搜索更新的EST序列,组装后设计特异引物在豫麦8679/红芒春31重组自交系群体(recombined inbreed lines,RILs)中鉴定与小麦穗粒数相关的CKX基因.结果表明,Tackx3基因在RILs群体中表现较好的多态性,并与小麦穗粒数相关.具有"A"型Tackx3等位基因的家系其穗粒数大都分布在较低的范围内(穗粒数15～60),平均值为55:而具有"B"型Tackx3等位基因的家系其穗粒数大都分布在较高的范围内(61～95),平均值为65,穗粒数均值T测验达极显著水平,说明Tackx3基因等位变异与小麦穗粒数形成关系密切.     

Molecular mapping of QTLs for domestication-related traits in cowpea (V. unguiculata (L.) Walp.)

Understanding the genetic basis underlying domestication-related traits (DRTs) of cowpea (Vigna unguiculata (L.) Walp.) is important since the genome has experienced divergent domestication and in addition it is also useful to utilize the wild germplasm efficiently for improving different traits of the cultivated cowpea. Quantitative trait loci (QTLs) for DRTs were identified in a population of 159 F₇ recombinant inbred lines derived from a cross between a domesticated cowpea (V. unguiculata (L.) Walp.) variety, 524B, and a wild accession, 219. Using the constructed linkage map, QTLs for 10 DRTs were analysed and mapped. QTLs for seed, pod and flower related traits were detected. Subsequently, QTL for ovule number was also identified. To our knowledge, this is the first time a QTL for this trait has been observed. QTLs for DRTs show co-localization on three linkage groups and pleiotropy or close linkage of genes for the traits is suggested in these chromosome regions. The information gained in this study can be used for marker-assisted selection of domestication-related QTLs in cowpea and enhance understanding of domestication in the genus Vigna.     

Deployment of wild relatives for genetic improvement in rice (Oryza sativa)

Rice is one of the most important crops in the world. The wild species of rice are expected to have novel beneficial alleles that have been lost from cultivated rice during the process of domestication. Therefore, wild species could be the potential source to induce lost genetic diversity in cultivated rice. Serving as an important reservoir of novel genes/QTLs, wild species, in general, are better adapted to different ecologies and can tolerate many biotic and abiotic stresses. Despite that, only a few wild species are studied and extensive characterization both at the molecular and morphological level is yet to be achieved. Several agronomically important genes/QTLs for improving biotic and abiotic stresses, resistance, productivity and grain quality traits were identified from AA genome donor wild species and were tagged with breeder friendly molecular markers for their transfer to elite genetic backgrounds. The present review provides information on the important wild rice species harbouring genes/QTLs for agriculturally important traits and their successful utilization in rice breeding programmes.     

植物矮生性状的分子遗传研究进展

近年来,随着分子生物学和基因组学的飞速发展,对作物高产性状,高产机理及其相关基因的研究愈加深入,应用基因工程技术对作物进行遗传改良已成为提高作物产量的有效途径,培育理想株型已成为作物育种的重要目标。株高是高等作物的重要农艺性状之一,植株过高容易引起倒伏而减产,而矮生植株抗倒能力强,高产,因而矮化育种对培育理想株型十分重要,矮生基因的发掘研究和利用也越来越受到重视。本文综述了目前高等作物矮生性的分子遗传研究进展,特别是对水稻、小麦、玉米、黄瓜、西瓜和番茄等主要作物矮生性状的遗传特点、分子标记、矮生基因的克隆等方面的研究进展做了较为详细的总结和评价,分析了激素对高等植物矮生突变体的调控,提出了高等植物矮生资源的利用和矮化育种中存在的问题,并探讨了高等植物矮生性状分子遗传学研究和分子育种的发展趋势。     

Application of cell and tissue culture and in vitro selection for disease resistance breeding — a review

Summary Somaclonal variation, i.e. the variation induced by cell and tissue culture, offers an opportunity to broaden the genetic variation of crops. As a result of somaclonal variation a wide range of plant characteristics can be altered. However, the selection of agronomically important traits, e.g. disease resistance, has many limitations. The efficiency of selection can be increased by the application of in vitro selection procedures. Selection strategies that may be applied to obtain disease resistant somaclonal variants are described. Their merits and limitations, in relation to the efficiency of the procedures, the frequency of disease resistant variants and the genetics of the resistance obtained, are discussed.     

Screening techniques and sources of resistance to parasitic angiosperms

Parasitic angiosperms cause great losses in many important crops under different climatic conditions and soil types. The most widespread and important parasitic angiosperms belong to the genera Orobanche, Striga, and Cuscuta. The most important economical hosts belong to the Poaceae, Asteraceae, Solanaceae, Cucurbitaceae, and Fabaceae. Although some resistant cultivars have been identified in several crops, great gaps exist in our knowledge of the parasites and the genetic basis of the resistance, as well as the availability of in vitro screening techniques. Screening techniques are based on reactions of the host root or foliage. In vitro or greenhouse screening methods based on the reaction of root and/or foliar tissues are usually superior to field screenings and can be used with many species. To utilize them in plant breeding, it is necessary to demonstrate a strong correlation between in vitro and field data. The correlation should be calculated for every environment in which selection is practiced. Using biochemical analysis as a screening technique has had limited success. The reason seems to be the complex host-parasite interactions which lead to germination, rhizotropism, infection, and growth of the parasite. Germination results from chemicals produced by the host. Resistance is only available in a small group of crops. Resistance has been found in cultivated, primitive and wild forms, depending on the specific host-parasite system. An additional problem is the existence of pathotypes in the parasites. Inheritance of host resistance is usually polygenic and its transfer is slow and tedious. Molecular techniques have yet to be used to locate resistance to parasitic angiosperms. While intensifying the search for genes that control resistance to specific parasitic angiosperms, the best strategy to screen for resistance is to improve the already existing in vitro or greenhouse screening techniques.     

Whitebacked planthopper Sogatella furcifera (Horváth) (Homoptera: Delphacidae) resistance in rice variety Sinna Sivappu

Whitebacked planthopper (WBPH) along with brown planthopper (BPH) has emerged as a major pest of rice in several Asian countries. Development and cultivation of varieties resistant to both planthoppers is an ecologically acceptable strategy to manage these pests. Sinna Sivappu, a Sri Lankan landrace, was reported to be resistant to both planthoppers. While inheritance of BPH resistance has been reported, the genetics of WBPH resistance in this variety is not known. Using a mapping population of 255 F_2:3 families from Taichung Native (TN)1/Sinna Sivappu cross and 128 polymorphic simple sequence repeat (SSR) markers, genes or quantitative trait loci (QTLs) for WBPH resistance quantified in ten phenotypic tests were identified, adopting classical Mendelian segregation, correlation and QTL analyses. The inheritance pattern suggested that a single recessive gene controlled regulation of seedling damage score. Antixenosis or nymphal preference was influenced by two complementary recessive genes, whereas tolerance in terms of days to wilt was under the influence of a single dominant gene. Several of these phenotypic tests recorded high degree of positive or negative correlation between them, suggesting dependence or redundancy of the tests. QTL analysis revealed 13 loci associated with nine traits. Five major-effect QTLs were detected for damage score (chromosome 6), nymphal survival (chromosome 12), and days to wilt (three QTLs on chromosome 4). We suggest involvement of four WBPH resistance genes in Sinna Sivappu, designated as wbph9(t), wbph10(t), wbph11(t), and Wbph12(t). One of the recessive genes could be allelic to any of the recessive genes reported in cluster C on chromosome 6 which might confer resistance to both BPH and WBPH.     

Recurrent selection as a breeding procedure for rye and other cross-fertilized plants

Summary The inadequacy of the established breeding methods (mass selection, family selection) and the fact that a breeding procedure based on heterosis is not feasible for all crops, have given the incentive to search for more effective breeding methods, in particular for cross-fertilized plants.On the basis of experiments with rye, the writer comes to the conclusion that a breeding system founded on the polycross test is somewhat unsatisfactory, because it leads too soon to a narrowing of the material, so that the degeneration caused by inbreeding cannot be avoided.Better possibilities are offered by the methods of recurrent selection developed for maize, particularly by those schemes initiating from two entirely unrelated populations (reciprocal recurrent selection). The two populations are subjected to a test cross system whereby individuals from one population are outcrossed on representative groups of individuals from the other one, and conversely. Tests of the progenies obtained in this way reveal which individuals from the population K combine well with population L, and vice versa. By following the line described in the article, a narrowed population K (indicated as K₁) and a narrowed population L (indicated as L₁) are obtained which more or less complement each other. This complementary character is enhanced by repeating the selection process. Crossing in mass of these two narrowed populations may result in a valuable hybrid which is best referred to as a varietal hybrid. It seems that here the danger of inbreeding is reduced to a minimum.This method has already yielded favourable results at the Plant Breeding Station of the Central Bureau at Hoofddorp c.f. Koopman (7). From the current experiments at the Institute of Agricultural Plant Breeding at Wageningen it also appears that by the breeding system described in this paper many fallacies of the old procedures are eliminated.     

Development of a recurrent apple breeding programme in New Zealand: a synthesis of results,and a proposed revised breeding strategy

This paper describes an apple breeding population that has been developed in New Zealand since 1990 to broaden the genetic base for cultivar breeding. The population is now in its third generation, with recurrent selection for general combining ability being the underlying approach. During the 20 years of the programme, nearly 1,000 trees have been progeny tested. An early focus on selection within open-pollinated tests has been replaced by selection within control-pollinated tests. Genetic evaluation methods along with estimates of genetic parameters (e.g. heritability, genetic correlations, and genotype-by-environment interactions), genetic gain, and genetic diversity are summarised in this paper. The third-generation crossing programme involving nearly 350 parents is almost completed and seedlings from these crosses are in the nursery. In the revised breeding strategy, three hierarchal populations are envisioned to better integrate this broad-based population with the more commercially focused cultivar breeding programme: main breeding population (MBP), elite breeding populations (EBP) and cultivar development populations (CDP). A two-subline structure and a minimum of two crosses per parent will be implemented in the MBP. EBP will focus on developing parents for breeding goals of the CDP. Forward-selected (based on estimated breeding values) candidates from the main- and elite populations will be used as parents of the CDP. Cloning of seedlings in elite populations and also in the first-stage of cultivar development, will be investigated as a tool for enhancing predictability and shortening the cycle for delivering genetic gain.     

Breeding for resistance to potato tuber moth,Phthorimaea operculella (Zeller), in diploid potatoes

Summary Sixty-two 2x families were generated by intermating 16, 2x clones and evaluated for resistance to potato tuber moth (PTM), Phthorimaea operculella under natural infestation in a storage at San Ramon, Peru and in laboratory tests. The following conclusions could be drawn: (1) relatively simple inheritance was observed for resistance derived from Solanum sparsipilum (spl), (2) the high level of resistance of the original spl has been transferred, undiminished, into an advanced 2x population, (3) simple phenotypic selection was successfully applied to transfer resistance into an improved 2x population, (4) there was a strong indication of reciprocal effects, however spl cytoplasm is not essential for the expression of nuclear resistance genes, (5) antibiosis and antixenosis are the mechanism of PTM resistance in this population, and (6) 4x × 2x crosses could be used to transfer the resistance into commercial cultivars.     

Efficient marker‐assisted backcross conversion of seed‐parent lines to cytoplasmic male sterility

For many crops, cytoplasmic male sterility (CMS) is a cornerstone of hybrid production. Efficient conversion of elite lines to CMS by marker‐assisted backcrossing is therefore desirable. In contrast to gene introgression, for which donor segments around target genes have to be considered, background selection for CMS conversion focuses solely on recovery of the recurrent parent genome. The optimal selection strategies for CMS conversion will consequently differ from those for gene introgression and have not yet been investigated. The objectives of our study were to evaluate and optimize the resource requirements of CMS conversion programmes and to determine the most cost‐effective use of single‐marker (SM) and high‐throughput (HT) assays for this purpose. We conducted computer simulations for CMS conversion of genetic models of sugar beet, rye, sunflower and rapeseed. CMS conversion required fewer resources than gene introgression with respect to population size, marker data points and number of backcross generations. Combining HT assays in early backcross generations with SM assays in advanced backcross generations further increased the cost‐efficiency of CMS conversion for a broad range of cost ratios.