Model legumes contribute to faba bean breeding

Faba bean is an excellent candidate crop to provide nitrogen input into temperate agricultural systems. However, its growth is hampered by several factors including environmental stresses and the presence of anti-nutritional factors. To solve these limitations, breeding programs have been initiated that were successful for monogenic traits but not so for multigenic traits. The large genome size of faba bean has slowed down breeding processes. Several other legumes have emerged as model legumes including Medicago truncatula, Lotus japonicus, Glycine max and Pisum sativum. The establishment of these models has already boosted our understanding of important processes such as the nitrogen-fixing symbiotic interaction. The high level of synteny and collinearity existing between legumes makes possible the transfer of key knowledge from model legumes to faba bean. Here we review the most recent knowledge gained from model legumes on grain quality, resistance to biotic and abiotic stresses, nitrogen-fixing symbiosis and how this knowledge can be employed for faba bean breeding.     

Breeding Differently—the Digital Revolution: High-Throughput Phenotyping and Genotyping

A conventional potato breeding strategy uses targeted outcrossing, followed by phenotypic recurrent selection over a series of generations to identify improved cultivars. This paper reviews recent research in Australia aimed at improving the efficiency of such breeding. To develop marker-assisted selection (MAS) for traits of interest, our initial targets were qualitative disease resistances for potato cyst nematode (Globodera rostochiensis Ro1), Potato virus Y and Potato virus X. We undertook a cost analysis comparison between MAS and conventional screening, confirming that MAS would be cost-effective within a breeding programme. Then, as the majority of target traits are quantitative in nature, we also looked at methods to address these traits, including progeny testing and a quantitative genetic analysis technique to develop estimated breeding values (EBVs). We found the markers were useful for detecting the disease resistance characters, while the EBVs improved the analysis of the complex traits. Using a combination of MAS, EBVs and conventional screening methods, we then designed a breeding scheme for rapid selection of cultivars with multiple desirable traits, reducing the breeding cycle from over 10 to 4 years. We then explored the factors that will affect the application of genomic selection in potato and investigated strategies to incorporate genomic selection in potato breeding, as we found that it would accelerate genetic gain as the breeding cycle can be reduced to 1 year. Improvements in computational power are also flowing on to research capabilities such as sequencing, high-throughput phenotyping and data analysis, which will accelerate germplasm improvement and breeding. High-throughput phenotyping facilities are being developed that include automated glasshouse systems equipped with imaging sensors and in-field high-throughput phenotyping systems with sensors mounted on ground- or aerial-based vehicles. Using these technological improvements in phenotypic and genotypic analysis will reduce the breeding cycle in a cost-effective manner and means that we can now breed differently.     

花生基因组资源的开发及应用

花生是世界主要的油料作物,但由于花生本身的遗传特性,导致其基因组资源的开发和利用存在较大难度。花生的高度闭花授粉、初级基因库遗传基础狭窄以及栽培种与二倍体近缘野生种之间的杂交不亲和性,导致花生栽培种的分子遗传多样性偏低,成为花生分子遗传改良的主要瓶颈。然而,近五年来,花生基因组资源开发迅速,分子标记的开发、遗传和物理图谱的构建、表达序列标签（ESTs）的产生、突变体资源的创建和功能基因组学平台的构建促进了QTL的鉴定以及与农艺性状相关的耐/抗生物和非生物胁迫基因的挖掘。本文概述了当前花生基因组资源的研究现状,并对下一步的发展方向进行了展望。     

Faba bean breeding for disease resistance

Faba bean is a major grain legume widely cultivated in many countries for food and feed purposes. A number of aerial fungi, together with soil-borne pathogens associated with foot and root rot complexes, nematodes, parasitic weeds and viruses may cause severe diseases in faba bean crops. The use of genetic resistance is the most economical and environmentally friendly control method. However, to date no efficient sources of resistance have been described to some diseases, or it is scarce and of complex nature, making necessary the implementation of other control measures. Phenotypic expression of resistance is usually poorly described. As a consequence of this, and of the poorly developed genomic resources available, the genetic basis of resistances is, in most cases, largely unknown. Effectiveness of MAS might soon increase with the adoption of new improvements in marker technology together with the integration of comparative mapping and functional genomics. In this paper we will review and critically discuss current and future strategies on breeding faba bean for disease resistance.     

Faba bean breeding for drought-affected environments: A physiological and agronomic perspective

The faba bean (Vicia faba L.) crop often experiences drought during its growth and development such that soil moisture deficits constrain its production. As droughts are predicted to increase in both frequency and intensity due to climate change, a better understanding of drought response patterns and associated traits is essential for obtaining yield stability in water-limited environments. This review deals with adaptation mechanisms associated with drought avoidance, escape and tolerance, with an emphasis on physiological traits such as stomatal conductance, carbon isotope discrimination and leaf temperature. Leaf temperature is considered an effective surrogate measure for other measures of stomatal characteristics. Drought tolerance through osmotic adjustment has not yet been demonstrated in faba bean although it is found in many other legumes including chickpea and pea. Deeper root growth, leading to uptake of otherwise unavailable water, helps the plant to avoid drought by delaying dehydration, but genetic variation and heritability of the trait are essentially unknown for faba bean. Crop management strategies, such as early planting, and appropriate phenology, are particularly important for drought escape in regions where terminal drought is common. Disease resistance is especially important in drought-prone areas to reduce the need for expensive control measures when yields are uncertain. The relevance of soil fertility status and nutrient availability are also covered. Drought escape and ascochyta blight resistance are important breeding objectives for terminal drought regions. Some form of drought resistance is necessary for the transient droughts experienced in most regions, and drought avoidance can be screened by a combination of leaf temperature or other rapid test of stomatal characteristics followed by carbon isotope discrimination in the most valuable materials. No single trait is adequate to improve yield in drought-prone environments, rather, a combination of characteristics is needed.     

Molecular marker-assisted selection for potato breeding

The use of molecular markers in potato breeding offers new opportunities for the selection of genotypes. To date, many markers linked to useful traits have been found. Indeed, the potato molecular map is saturated with more than 350 markers uniformly distributed on 12 chromosomes. More than 25 single dominant genes have been localized on the potato map, most of them being pest-resistance genes, together with some quantitative trait loci (QTL) controlling yield and tuber quality traits. Molecular markers linked to these genes are now available for rapid, efficient assisted selection (positive assisted selection). Moreover, in order to transfer useful genes, interspecific crosses between wild and cultivated genotypes are often performed, and in this case the use of species-specific molecular markers would allow the wild genomic content to be reduced in few backcross generations (negative assisted selection). The following review discusses the progress achieved in potato breeding through molecular marker-assisted selection.     

Growth,yield and nitrogen performance of faba bean intercrops with oat and triticale at varying seeding ratios

Intercropping of grain legumes with cereals may offer several advantages over sole crops for forage production and is commonly used, particularly in low‐input agriculture. Faba bean (Vicia faba L.), oat (Avena sativa L.) and triticale (×Triticosecale Wittmack) sole crops as well as the intercrops of faba bean with each of the above cereals, in three seeding ratios (75:25, 50:50 and 25:75), were compared for dry‐matter (DM) yield, nitrogen (N) concentration, chlorophyll content, growth rate and plant height in a 2‐year field experiment. Triticale sole crop and faba bean intercrops with triticale provided higher DM yield than faba bean sole crop and the intercrops of faba bean with oat. Growth rates of faba bean, oat and triticale in mixtures were lower than those in sole crops. Faba bean plants were taller in the intercrops than in the sole crop at 3 weeks after tillering (WAT), whereas at 6 WAT, the trend was different as faba bean plants in the sole crop were taller than in the intercrops. N concentration was higher for the cereals when faba bean was included in the mixture. Crude protein (CP) concentration was the highest in faba bean sole crop followed by the faba bean intercrops with oat. However, triticale sole crop and faba bean mixtures with triticale provided higher CP yield than all other crops because of their highest DM yield. Thus, mixtures of faba beans with triticale could be a promising alternative for increased forage production because of their capacity for high DM and protein yields.     

Use of Major Quantitative Trait Loci to Improve Grain Yield of Rice

Further improvement of rice productivity remains a challenge. Breeding is perceived as an important option to increase rice yield. However, the genetic progress of grain yield in most rice breeding programs was slow in the last decades. Although great progress in rice genomics and molecular biology has been achieved, the effect of such technological innovations on rice breeding is far small. Marker-assisted selection （MAS） for a few target quantitative trait loci （QTLs） has significant effects in improving qualitative traits, such as disease resistance. The success of MAS has therefore motivated breeders to identify and use major QTLs for yield and yield component traits. In this review, we summarized the recent methods in QTL identification, including novel statistical methods for linkage and association mapping, special population types, and whole-genome sequencing. We reviewed the successful application of marker-assisted gene introgression and gene pyramiding to improve grain yield and discussed the design of efficient MAS schemes to further increase the success rate of breeding programs. The use of well-characterized major QTLs through introgression and gene pyramiding is proven effective in improving grain yield, particularly yield under abiotic stress. Major QTLs that are stable across genetic background and growing environments are often found in less adapted germplasms, such as landraces and wild relatives. Advanced backcross QTL analysis and introgression lines, which integrate QTL discovery and utilization, are important methods for exploiting major QTLs contained in such germplasms. Next-generation sequencing substantially increases mapping resolution and accelerates the identification of casual genes underlying major QTLs. Practical guidelines derived from theoretical and empirical studies are given to guide the design of efficient marker-assisted gene introgression and pyramiding schemes.     

小麦水分高效利用分子育种研究进展

干旱缺水是引起全球作物减产的主要自然灾害。小麦水分高效利用遗传改良是一个重大课题。本文对小麦水分高效利用分子标记、功能基因克隆鉴定、转基因、分子设计育种等方面的国内外研究进展进行了综述。在小麦中已经鉴定出A组染色体上存在控制水分利用效率的QTL;开发出与TaSAP1等基因紧密连锁的功能标记;克隆了转录因子基因TaWRKY并对其抗旱抗逆功能进行了鉴定;转HVA1和DREB等基因的小麦可以明显提高水分高效利用能力;利用水旱地品种进行轮回杂交结合分子标记辅助选择育种技术进行了小麦水分高效利用分子设计育种初探。以上研究进展为小麦水分高效利用遗传改良提供了理论依据和技术支撑。     

Cisgenesis,a New Tool for Traditional Plant Breeding,Should be Exempted from the Regulation on Genetically Modified Organisms in a Step by Step Approach

Modern potato breeding requires over 100,000 seedlings per new variety. Main reasons are (1) the increasing number of traits that have to be combined in this tetraploid vegetatively propagated crop, and (2) an increasing number of traits (e.g., resistance to biotic stress) originates from wild species. Pre-breeding by introgression or induced translocation is an expensive way of transferring single traits (such as R-genes, coding for resistance to biotic stress) to the cultivated plant. The most important obstacle is simultaneous transfer of undesired neighbouring alien alleles as linkage drag. Stacking several genes from different wild sources is increasing this linkage drag problem tremendously. Biotechnology has enabled transformation of alien genes into the plant. Initially, transgenes were originating mainly from microorganisms, viruses or non-crossable plant species, or they were chimeric. Moreover, selection markers coding for antibiotic resistance or herbicide resistance were needed. Transgenes are a new gene source for plant breeding and, therefore, additional regulations like the EU Directive 2001/18/EC were developed. Because of a strong opposition against genetic modification of plants in Europe, the application of this Directive is strict, very expensive, hampering the introduction of genetically modified (GM) crops and the use of this technology by small and medium-sized enterprises (SMEs). Currently, GM crops are almost the exclusive domain of multinationals. Meanwhile, not only transgenes but also natural genes from the plant species itself or from crossable plant species, called cisgenes, are available and the alien selection genes can be avoided in the end product. This opens the way for cisgenic crops without alien genes. The existing EU directive for GM organisms is not designed for this new development. The cisgenes belong to the existing breeders’ gene pool. The use of this classical gene pool has been regulated already in agreements regarding breeders’ rights. We are proposing a step by step approach starting with a crop and gene specific derogation and monitoring towards a general exemption of cisgenic plants from the Directive. Two examples, i.e. development of cisgenic potato for resistance to Phytophthora infestans and cisgenic apple for resistance to Venturia inaequalis are discussed shortly for illustration of the importance of cisgenesis as a new tool for traditional plant breeding. Cisgenesis is simplifying introgression and induced translocation breeding tremendously and is highly recommended for SMEs and developing countries.     

Integration of genomics approach with traditional breeding towards improving abiotic stress adaptation: drought and aluminum toxicity as case studies

Traditional breeding efforts are expected to be greatly enhanced through collaborative approaches incorporating functional, comparative and structural genomics. Potential benefits of combining genomic tools with traditional breeding have been a source of widespread interest and resulted in numerous efforts to achieve the desired synergy among disciplines. The International Center for Tropical Agriculture (CIAT) is applying functional genomics by focusing on characterizing genetic diversity for crop improvement in common bean (Phaseolus vulgaris L.), cassava (Manihot esculenta Crantz), tropical grasses, and upland rice (Oriza sativa L.). This article reviews how CIAT combines genomic approaches, plant breeding, and physiology to understand and exploit underlying genetic mechanisms of abiotic stress adaptation for crop improvement. The overall CIAT strategy combines both bottom-up (gene to phenotype) and top-down (phenotype to gene) approaches by using gene pools as sources for breeding tools. The strategy offers broad benefits by combining not only in-house crop knowledge, but publicly available knowledge from well-studied model plants such as arabidopsis [Arabidopsis thaliana (L.) Heynh.]. Successfully applying functional genomics in trait gene discovery requires diverse genetic resources, crop phenotyping, genomics tools integrated with bioinformatics and proof of gene function in planta (proof of concept). In applying genomic approaches to crop improvement, two major gaps remain. The first gap lies in understanding the desired phenotypic trait of crops in the field and enhancing that knowledge through genomics. The second gap concerns mechanisms for applying genomic information to obtain improved crop phenotypes. A further challenge is to effectively combine different genomic approaches, integrating information to maximize crop improvement efforts. Research at CIAT on drought tolerance in common bean and aluminum resistance in tropical forage grasses (Brachiaria spp.) is used to illustrate the opportunities and constraints in breeding for adaptation to abiotic stresses.     

Progress of CRISPR/Cas9 technology in breeding of Brassica napus

Gene editing technology provides important technical basics for the research in plant functional genes and crop genetic improvement. CRISPR/Cas9-mediated gene editing is an effective experimental tool for crop genome directed editing in recent years, which has been widely used in many crops as rice, wheat and other crops. CRISPR/Cas9 system was expected to be a powerful experimental tool in genetic improvement and molecular design breeding of rapeseed. This paper, which based on the development history and the latest research of CRISPR/Cas9-mediated gene editing technology in rapeseed, summarized the progress of CRISPR/Cas9 including plant type improvement, yield traits, quality improvement, disease and stress resistance improvement, yellow seed creation and other utilizes at present. The application scope, development direction and target analysis method of this technology in rape were focused. The problems of CRISPR/cas9 system in rapeseed breeding were analyzed and the improvement strategies were discussed. Finally, views on direction of rapeseed breeding by gene editing were emphasized.     

分子标记辅助选择在小麦抗病和品质遗传育种中的应用

DNA水平的分子标记技术能够提供便捷、准确、稳定的遗传标记.近年来,在小麦中应用分子标记进行遗传图谱构建、定位目标基因以及鉴定外源染色体片段等方面发挥了重要作用.为了给相关研究提供参考,本文就分子标记技术在小麦抗条锈、叶锈和白粉病以及小麦麦谷蛋白、淀粉、硬度等品质方面的作用及应用进展进行了阐述,并对分子标记辅助选择在育种应用中存在的问题进行了论述.     

Application of Molecular Markers in Breeding for Nitrogen Use Efficiency

Summary

Nitrogen use efficiency (NUE) is defined as dry matter yield produced per unit of N supplied and available in the soil. NUE is approximately 33% for cereal production worldwide. Increased cereal NUE must accompany increased yield needed to feed the growing world population. Consequently, continued efforts are needed to include plant selection under low N input which is not often considered a priority by plant breeders. Molecular markers have accelerated plant breeding in a number of areas including biotic (disease and insect) resistance and abiotic (drought, low nitrogen fertilization and frost) tolerance. Marker-based technology has already provided scientists with a powerful approach for identifying and mapping quantitative trait loci (QTL) and would lead to the development of a better understanding of genetic phenomena. Two main NUE studies have been discussed. The first study identified QTL for NUE in maize involved the grain yield and secondary morphological traits of interest, such as plant height, ear leaf area, ears per plant and kernels per ear. This was compared with second study of QTL for yield and its components with genes encoding cytolistic gult-amine synthestase and leaf N0₃ ^- content. These secondary traits were correlated with yield and demonstrated segregation with high heritability under low nitrogen conditions. Marker assisted selection (MAS) should be able to offer significant advantages in cases where phenotypic screening is particularly expensive or difficult, including breeding projects involving multiple genes, recessive genes, late expression of the trait of interest, seasonal considerations, or geographical considerations. In addition to reducing costs of conventional breeding, MAS also has the potential to generate time savings. Possibly, the greatest contribution of QTL mapping to plant breeding will be the basic understanding of the genetic architecture of quantitative traits, thereby relating specific genetic loci with the biological mechanisms associated with desirable phenotypes.     

广谱抗稻瘟病种质75-1-127的褐飞虱抗性基因鉴定及分子标记辅助选择育种

【目的】水稻品系75-1-127携带广谱抗稻瘟病基因Pi9,已被广泛应用于抗稻瘟病水稻品种改良。笔者育种实践发现75-1-127表现出较强的褐飞虱抗性,因此鉴定该品系中的褐飞虱抗性基因并进行分子辅助选择育种。【方法】根据水稻品系B5中褐飞虱抗性基因Bph14和Bph15的序列,设计引物扩增75-1-127的基因组DNA,并对PCR产物进行测序分析。采用苗期集团法鉴定了75-1-127和B5的褐飞虱抗性表型。利用与Bph14与Bph15连锁的分子标记筛查了75-1-127为稻瘟病抗源回交转育的两系不育系后代,并鉴定了这些后代的稻瘟病抗性、褐飞虱抗性和主要农艺性状。【结果】75-1-127中含有与B5完全一致的Bph14和Bph15序列。75-1-127和B5苗期褐飞虱抗性均为1级。在以75-1-127为抗源改良的两系不育系中,携带Bph14、Bph15的单基因系或双基因系的褐飞虱抗性均得以改良,其中双基因聚合系的死苗率为8.5%,与供体亲本75-1-127以及阳性对照B5差异不显著,进一步证实75-1-127含有褐飞虱抗性基因。【结论】水稻品系75-1-127携带褐飞虱抗性基因Bph14和Bph15,可以作为抗源应用于水稻褐飞虱抗性育种。     

花生遗传图谱构建与QTL定位研究进展

遗传图谱构建与QTL定位对花生分子育种具有十分重要的意义.随着分子标记与测序技术的快速发展,极大地促进了花生重要数量性状的研究进程,并获得了一些与抗病、产量等重要性状相关联的分子标记.本文对国内外花生的分子标记开发、遗传图谱构建以及QTL定位的研究进展进行了综述,为花生分子标记辅助选择,提高花生育种效率,加速育种进程提供了理论参考.     

野生稻高产QTL的分子标记辅助育种进展

1995年中国国家杂交水稻工程技术研究中心与美国康奈尔大学合作,在马来西亚普通野生稻中鉴定出两个主效高产QTLyld1.1和yld2.1.随后将野生稻高产QTL导入优良晚稻恢复系测64-7及中稻恢复系9311和明恢63中,采用分子标记辅助选择与田间选择相结合,育成了Q611等携带野生稻高产QTL yld1.1和yld2.1的新恢复系.经测交鉴定,Q611所配组合表现出强大的产量优势,说明野生稻高产QTL具有显著的增产效应和重要的育种价值,同时也表明采用分子标记辅助选择方法对数量性状进行遗传改良同样具有明显的效果.     

三系杂交水稻抗稻瘟病、白叶枯病育种研究进展

目前多数三系杂交稻组合抗病性较差,其抗病性受恢复系与不育系的共同影响,提高杂交稻抗性的关键是向三系亲本同步导入抗性基因.目前杂交稻的抗病育种基本立足于常规育种,但常规抗病育种方法存在一定的局限性;分子标记辅助选择在三系亲本抗病单基因导入和多基因聚合育种中均取得较大进展.针对存在的问题提出了抗病育种研究策略.     

Molecular Diagnostics for Complex Pest and Disease Resistance and Tuber Quality Traits: Concept,Achievements and Perspectives

We summarize the concept of molecular diagnostic of complex traits related to pest and disease resistance and to tuber quality of potato, and describe recent achievements and perspectives. Many potato characteristics are controlled by multiple genetic and environmental factors. Knowing the genes and their allelic variants that underlay these characteristics allows developing molecular diagnostic tools to select for improved potato cultivars. Diagnostic DNA-based markers can be used to identify superior genotypes (precision breeding). Diagnostic markers can be identified by combining quantitative trait locus mapping, candidate gene mapping and association mapping using functional and positional candidate genes as markers. This approach was successfully used to identify loci, which contribute to the natural variation of important agronomic traits, including resistance against root cyst nematodes, late blight and wart disease and tuber quality (resistance to bruising and chip colour). In the future, whole genome association mapping based on single-nucleotide polymorphism genotyping methods in combination with the annotated potato genome sequence will allow identifying additional genes and gene variants controlling agronomic performance in potato. Prerequisites are accurate phenotyping under field conditions of advanced breeding materials, cost-effective and reliable genome-wide genotyping methods, and user-friendly software tools allowing to extract knowledge from massive quantities of data. This will further facilitate molecular diagnosis, selection and combination of superior alleles in potato-breeding programmes.     

Diversity maintenance and use of Vicia faba L. genetic resources

The faba bean (Vicia faba L.) is an ancient crop that is represented in collections by cultivated forms only. Botanic and molecular data suggest that the wild ancestor of this species has not yet been discovered or has become extinct. This fact makes ex situ collections more crucial for the present and future breeding activities of this crop, especially when the modernization of agriculture reduces genetic diversity.