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.     

大豆种质5621对所衍生品种的遗传贡献

自1961年辽宁大豆种质5621育成后，由5621作为直接亲本先后衍生出7个优良大豆品种，进而由这7个大豆品种衍生出26个品种，在这33个大豆品种中，有15个曾获国家级或省部级科技成果奖励。5621对其衍生品种的遗传贡献主要来自细胞核，仅有6个品种承带5621的细胞质，细胞质的遗传贡献较小。     

木薯种质基因型与环境互作分析

为加强木薯现有选育材料和引进种质的研究利用,准确评价各种质产量相关性状的稳定性和适应性,以木薯主栽品种华南8号(SC8)和华南205号(SC205)为对照,选用138份选育材料和8份瑞士引进新种质,应用AMMI模型对连续3年的干物质率、收获指数的遗传方差、环境方差和遗传与环境(G×E)互作进行探讨。结果表明:(1)比对照SC8的干物质率和收获指数更高且更加稳定的种质分别有4份和6份,比对照SC205的干物质率和收获指数更高且更加稳定的种质分别有61份和12份;(2)对干物质率的分析中有67份种质比SC8和有132份种质比SC205对不同年度环境的适应性更好,对收获指数的分析中有48份种质比SC8和有28份种质比SC205对不同年度环境适应性更好。AMMI模型很好地解释了木薯干物质率和收获指数的基因型G效应、环境E效应和G×E互作效应。该结果对木薯种质的环境敏感度和种植范围评估提供了依据。     

Variation in qualitative and quantitative traits of cassava germplasm from selected national breeding programmes in sub-Saharan Africa

An improved understanding of phenotypic variation within cassava germplasm in southern, eastern and central Africa will help to formulate knowledge-based breeding strategies. Thus, the overall objective of this study was to examine the phenotypic variation in cassava germplasm available within six breeding programmes in Africa, namely Uganda, Kenya, Tanzania, Rwanda, Democratic Republic of Congo and Madagascar. In each country, single-row plots were used for assessment of 29 qualitative traits and evaluation of four quantitative traits: root dry matter content (DMC), harvest index (HI), leaf retention (LR) and root cortex thickness. Qualitative traits provided limited discrimination of cassava germplasm. However, differences in DMC, HI, LR and root cortex thickness were observed among the germplasm indicating scope for genetic improvement. Highest average DMC was registered in Uganda (39.3%) and lowest in Tanzania (30.1%), with the elite genotypes having a relatively higher DMC than local genotypes. Highest average HI was observed in Uganda (0.60) and lowest in Kenya (0.32). Cassava genotypes displayed varied root peel thickness (0.34-4.89 mm). This study highlights variation in agronomic traits that could be exploited to increase cassava productivity.     

Leaf retention and cassava productivity

Increased longevity of leaves, or improved leaf retention, has been suggested as a possible means to increase productivity of cassava (Manihot esculenta Crantz). This study evaluated variation in leaf retention and its relation to cassava productivity under irrigated and stressed conditions. In the first trial 1350 clones were evaluated on the North Coast of Colombia with a 5-month dry period towards the end of the growth cycle. Clones with the leaf retention trait produced more total fresh biomass and yielded 33% more root dry matter than plants without the trait. In the irrigated trial 110 clones were evaluated on the CIAT farm at about 1000 mamsl. Leaf retention was quantified using a 1–5 visual score with five corresponding to excellent leaf retention. Genetic correlations between leaf retention and fresh foliage production (0.49), root dry matter yield (0.46), fresh root production (0.43) and root dry matter content (0.25) were obtained. Increased root yield under stressed and unstressed conditions was associated with increased total biomass production and increased harvest index. These finding concur with the results of cassava growth models that include leaf longevity as a variable. The lack of any negative genetic correlations between leaf retention and useful agronomic traits coupled with the relatively high genetic correlation for root yield and the high heritability (0.55) for leaf retention indicate that it should be relatively easy and advantageous to incorporate this characteristic in breeding and selection programs directed to increasing root yield under both water stressed and unstressed conditions.     

Emergence, spread and strategies for controlling the pandemic of cassava mosaic virus disease in east and central Africa

During the 1990s, an epidemic of an unusually severe form of cassava mosaic virus disease (CMD) has expanded to cover virtually all of Uganda, and substantial areas in the neighbouring countries of Kenya, Tanzania, Sudan and the Democratic Republic of Congo. Losses in the generally sensitive local cassava cultivars have been so great that a common farmer response to the problem has been the temporary abandonment of cassava cultivation. As a consequence, the CMD ‘pandemic’ has had a significant destabilising effect on food security in East Africa. In attempting to combat the problem, vigorous efforts have been made to identify, multiply and disseminate resistant cassava germplasm. This has included cultivars obtained from the breeding programme of the International Institute of Tropical Agriculture (IITA), based in Nigeria, as well as local selections derived from IITA parent stock. Whilst considerable success has been realised in controlling the pandemic in Uganda, addressing the problem at the regional level remains a major challenge. This article reviews progress made in recent years, both in understanding the cause and mechanisms behind the pandemic's expansion, and in developing strategies to control it. Particular attention is drawn to the likely threat the pandemic poses to cassava production in the countries of central Africa, most notably the Democratic Republic of Congo, where insecurity currently impedes an assessment of the problem and the ready implementation of control measures. Scientists and other stakeholders with an interest in CMD management are therefore urged to explore innovative mechanisms that will allow them to develop a more comprehensive approach to CMD control in the region.     

Closing the cassava yield gap: An analysis from smallholder farms in East Africa

Cassava yields in Africa are small and it remains unclear which factors most limit yields. Using a series of farm surveys and on-farm and on-station trials in Uganda and western Kenya, we evaluated the importance of abiotic, biotic and associated crop management constraints for cassava production in a range of socio-economic settings as found in smallholder farms in the region. Average yields under farmer management were 8.6 t ha⁻¹, but these were more than doubled to 20.8 t ha⁻¹ by using improved crop establishment, improved genotypes and 100–22–83 kg ha⁻¹ of single-nutrient N–P–K fertilizers. A farm survey revealed large yield differences between farms. Less endowed farmers harvested less cassava per unit area than better endowed farmers (difference of 5.9 and 9.7 t ha⁻¹ in Kenya and Uganda, respectively); differences were associated with less access to labour, poorer soils, and premature harvesting by less endowed farmers. Analysis of 99 on-farm and 6 on-station trials showed that constraints for cassava production varied strongly between sites and years. Poor soil fertility, early water stress and sub-optimal weed management limited cassava production by 6.7, 5.4 and 5.0 t ha⁻¹, respectively, when improved crop establishment and genotypes were used. Pests and diseases were relatively unimportant, while weed management was particularly important in farmer fields during a dry year in Kenya (yield gap of 11.6 t ha⁻¹). The use of complementary analytical tools such as multiple regression and boundary line analysis revealed that many fields were affected by multiple and interacting production constraints. These should be addressed simultaneously if significant productivity improvements are to be achieved. This will be more difficult for less endowed than for better endowed farm households, since the former lack social and financial capital to improve management.     

The effects of plant arrangement and density on intercropped beans (Phaseolus vulgaris) and maize I. Traits related to dry matter and seed productivity

In traditional agricultural practice in the tropics, climbing beans (Phaseolus vulgaris L.) and maize (Zea mays L.) are commonly grown together in hills (relatively widely spaced clumps of plants) rather than in rows. Density of planting is also low in many cases (average 3 plants per m² each of beans and maize in Colombia). Three experiments were conducted at CIAT in Cali, Colombia, to compare planting systems. Planting in hills significantly reduced lodging of the maize in two out of three experiments. Higher bean density also tended to reduce maize lodging due to an anchoring effect of the climbing stems. Maize yields were reduced by planting in hills in two out of three experiments, but tended to increase slightly with bean density. Bean yield was also reduced by planting in hills but increased with density up to 9 plants per m², associated with a reduction in node number per plant, especially on the branches. Bean harvest index was increased by planting in hills, but reduced by higher bean density. Bean cultivars significantly affected maize yield, which was negatively related to bean plant height and node number. The best-yielding bean cultivar (G2525) had a well-developed climbing main stem; it gave 53% greater yield than G4017, which had well-developed branches. There were no significant interactions of bean cultivars with spacing or density. Increased bean density, either in hills or in rows, had beneficial effects both on bean and maize yields, the latter mainly due to reduced lodging. Reducing the spacing between hills and increasing bean density has potential for increasing the total productivity of this cropping system.     

Increased productivity through integrated soil fertility management in cassava–legume intercropping systems in the highlands of Sud-Kivu,DR Congo

Smallholder farmers in sub-Saharan Africa are confronted by low productivity and limited investment capacity in nutrient inputs. Integrated soil fertility management (ISFM) aims at increased productivity through the combined use of improved germplasm, judicious fertilizer application and organic matter management, adapted to the local farming conditions. We hypothesize that the application of these different ISFM components can result in significant increases in productivity and economic benefits of cassava–legume intercropping systems. Participatory demonstration trials were conducted in the highlands of Sud-Kivu, DR Congo with 12 farmer groups during 3 seasons. Treatments included the farmers’ common practice (local common bean and cassava varieties, seed broadcast and manure addition) and sequentially added ISFM components: improved bean and cassava germplasm, modified crop arrangements, compound NPK fertilizer application and alternative legume species (groundnut or soybean). The use of improved germplasm did not result in yield increases without simultaneous implementation of other ISFM components. Modifying the crop arrangement by planting cassava at 2 m between rows and 0.5 m within the row, intercropped with four legume lines, increased bean yields during the first season and permits a second bean intercrop, which can increase total legume production by up to 1 t ha⁻¹ and result in an additional revenue of almost 1000 USD ha⁻¹. Crop arrangement or a second legume intercrop did not affect cassava storage root yields. Fertilizer application increased both legume and cassava yield, and net revenue by 400–700 USD ha⁻¹ with a marginal rate of return of 1.6–2.7. Replacing the common bean intercrop by groundnut increased net revenue by 200–400 USD ha⁻¹ partly because of the higher market value of the grains, but mostly due to a positive effect on cassava storage root yield. Soybean affected cassava yields negatively because of its high biomass production and long maturity period; modifications are needed to integrate a soybean intercrop into the system. The findings demonstrate the large potential of ISFM to increase productivity in cassava–legume systems in the Central-African highlands. Benefits were, however, not observed in all study sites. In poor soils, productivity increases were variable or absent, and soil amendments are required. A better understanding of the conditions under which positive effects occur can enable better targeting and local adaptation of the technologies.     

玉米育种目标的诱导创新因素

在市场经济条件下,农产品的市场需求和投入品的相对稀缺是诱导技术创新的主要因素,在我国,继续提高产量是技术采用的首要决定因素;但提高农民的经济收入会使其因素显得越来越重要。种质扩增、种质改良和种质创造是第一个重要的技术创新方向。第二是改善玉米品质。第三是培育抗逆境的新自交系和杂交种。耐旱、抗病和适宜的生育期都是我国玉米育种必须优先考虑的重要因素。     

玉米育种目标的诱导创新因素1,2

在市场经济条件下,农产品的市场需求和投入品的相对稀缺是诱导技术创新的主要因素。在我国,继续提高产量是技术采用的首要决定因素;但提高农民的经济收入会使其他因素显得越来越重要。种质扩增、种质改良和种质创新是第一个重要的技术创新方向。第二是改善玉米品质。第三是培育抗逆境的新自交系和杂交种。耐旱、抗病和适宜的生育期都是我国玉米育种必须优先考虑的重要目标。     

Susceptibility of potato varieties and advanced breeding lines (Solanum tuberosum L.) toPhytophthora infestans (Mont.) de Bary in greenhouse screenings

Late blight (Phytophthora infestons (Mont.) de Bary) has re-emerged as an important pathogen of the cultivated potato (Solanum tuberosum subsp.tubero-sum L.) in North America. The purpose of this study was to evaluate the relative susceptibility of potato germplasm in the greenhouse in order to initiate a breeding program for resistance to the US-8/A2 mating type which is the more aggressive and prevalent strain of late blight. Whole plants of 147 cultivars and breeding lines were evaluated. Percent plant area infection was visually assessed. Seven days after inoculation, infection ranged from 0 to 100% and the overall mean was greater than 50%. Two-thirds of the cultivars and breeding lines tested were very susceptible to the US-8 genotype. The highest resistance was identified in the somatic hybrids betweenS. tuberosum andS. bulbocastanum and their backcross derivatives. Pike and Snowden were less susceptible than the other North American cultivars. Zarevo was most resistant among the European cultivars. Seven of the advanced breeding lines were equivalent to Zarevo in infection levels. The host plant resistance identified among the material tested in this study can be used by breeding programs to develop improved cultivars with resistance to US-8 genotypes of late blight.     

茶树遗传育种研究进展

本文从茶树育种材料创新、育种鉴定技术发展、育种目标变化、育种程序的改进、育种成果以及良种繁育与推广体系等方面综述了茶树遗传育种领域的研究进展,为进一步深入开展茶树遗传育种研究提供参考。茶树育种材料创新的手段仍然以杂交为主,理化诱变的应用日趋广泛,转基因技术有待进一步完善。高分辨率检测设备和基因鉴定技术的应用,结合计算机预测模型开发,使茶树品种早期鉴定的准确性得到提升。茶树育种目标经过了高产、优质、早生的阶段,发展到了满足多样化需求的时期。进一步提高早期鉴定准确度、缩短育种周期是茶树育种技术发展的目标。     

狼尾草属牧草育种及分子生物学研究进展

狼尾草属植物不仅可以作为牧草，而且还是热区重要的粮食作物，因而得到广泛深入的研究。本文查阅了大 量的文献，介绍国内外狼尾草属牧草，主要包括珍珠粟和象草的种质资源、育种、组织培养、遗传多样性、基因克隆、 转基因、转录组和基因组学方面的研究现状，为未来狼尾草的研究提供参考，并对国内狼尾草育种及研究提出展望。     

基于EST-SSR标记的黄淮海和南方大豆育成品种遗传多样性研究

以我国黄淮海和南方大豆产区的153份大豆育成品种为材料,选用26对EST-SSR分子标记通过Power Marker V 3.25等软件对其进行遗传多样性、相似性与特异性分析。结果表明:153份大豆共检测到238个等位变异,变幅3~25个,平均8.1个;多态信息量变幅0.15~0.87,平均0.61;遗传变异丰富。基于EST-SSR分子标记的聚类分析将153个材料聚为3大类13小类。特异性分析表明,黄淮海产区的育成品种的特有等位变异较南方产区的多,特缺等位变异要少于南方,1991-2000年的特有等位变异最多;随着时间的推移,大量的外来育种材料应用于大豆育种,大豆育成品种的遗传基础有所拓宽。EST-SSR标记适用于大豆育成品种遗传多样性研究,研究结果可以为以后大豆种质资源保存与新品种的选育提供分子水平上的理论支持。     

马铃薯国外引种的探讨和建议

自1934年以来,我国共引进国外马铃薯普通栽培品种(系)1 315份,90余个杂交组合的实生种子100余万粒,野生种和原始栽培种共13个种的无性系110份,这些种质资源中许多已被直接或间接用于生产或育种。其中,通过多年多点鉴定直接用于生产的品种32个,从引进的杂交实生种子经系统选育推广的品种10余个,直接用于马铃薯有性杂交的国外资源占亲本总数的90%以上,诸多国外品种已成为我国高产、优质和多抗育种的骨干亲本。因此,加强国外马铃薯资源的引进、评价和利用,对于丰富我国马铃薯种质资源遗传基础意义重大,也是应对生物资源国际竞争日益激烈的战略决策。本文在总结我国马铃薯国外引种成就基础上,根据马铃薯国外引种出现的新情况,提出今后强化引种的建议。     

基于CRISPR/Cas9技术创制木薯MeSTP7和MeSTP15双基因突变体

木薯(Manihot esculenta Crantz)是一种热带、亚热带重要的粮食与能源作物,提高木薯的产量对木薯产业发展至关重要.木薯块根的发育直接影响其产量情况,而不同逆境胁迫会影响木薯块根的发育情况.因此解析木薯块根的发育机制有助于通过分子育种手段实现木薯高产,以及获得具备一定抗逆品质的优良种质,增强木薯的适应...     

玉米78599种质的杂优模式及其改良利用

玉米新种质的引入,改变了我国种质资源匮乏、遗传基础狭窄的育种现状。通过分析78599种质选育的自交系及其代表品种,总结出78599种质的主要杂种优势模式,即78599种质×改良Reid、78599种质×旅大红骨、78599种质×塘四平头、78599种质×Lancaster、78599种质×其它种质。介绍了78599种质在我国的改良利用情况,提出了78599种质在今后我国育种中的利用思路。     

A Review on Current Status and Future Prospects of Winged Bean (<Emphasis Type="Italic">Psophocarpus tetragonolobus</Emphasis>) in Tropical Agriculture

Winged bean, Psophocarpus tetragonolobus (L.) DC., is analogous to soybean in yield and nutritional quality, proving a valuable alternative to soybean in tropical regions of the world. The presence of anti-nutritional factors and high costs associated with indeterminate plant habit have been major concerns in this crop. But occurrence of good genetic variability in germplasm collections offers precious resources for winged bean breeding. However, lack of germplasm characterization is hindering such efforts. From a genomic standpoint, winged bean has been little studied despite rapid advancement in legume genomics in the last decade. Exploiting modern genomics/breeding approaches for genetic resource characterization and the breeding of early maturing, high yielding, determinate varieties which are disease resistant and free of anti-nutritional factors along with developing consumer friendly value-added products of local significance are great challenges and opportunities in the future that would boost cultivation of winged bean in the tropics. We review past efforts and future prospects towards winged bean improvement.     

木薯间作套种穿心莲高效栽培技术

木薯作为全球重要的薯类作物,既是热带地区粮食安全的保障,也是重要的淀粉工业原料。为促进木薯产业的发展,提高木薯种植比较经济效益,根据我区木薯间作套种中药材穿心莲在平南县的种植管理经验,总结出一套成熟的木薯间作套种穿心莲栽培技术,为木薯间作套种规范化栽培和生产提供技术支撑。