Breeding rice for rice yellow mottle virus resistance in Sub-Saharan Africa: a review

Rice is the world’s second most produced staple cereal crop after wheat. Currently, rice production and consumption have steadily increased in Sub-Saharan Africa (SSA). To date, rice is the largest imported commodity crop in the region. The low productivity is due to a number of biotic and abiotic stresses, and socio-economic constraints. Among the biotic constraints, rice yellow mottle virus (RYMV) is the most important constraint to rice in SSA. In SSA, RYMV causes yield losses ranging from 20% to 100%. Various control strategies (host resistance, cultural practices and chemicals) have been recommended to manage RYMV epidemics. RYMV disease management through generic crop protection chemicals is not economic nor is it successful due to the presence of a large number of vector species disseminating the virus. In addition, cultural practices are ineffective against RYMV because the virus is spread by several agents, including insect vectors. The use of RYMV resistant cultivars remains the most effective, economic and environmentally friendly method for resource poor farmers. However, RYMV resistant varieties have not yet been developed and deployed in SSA. The aim of this review was to present the main components in the development of rice cultivars with RYMV disease resistance. The paper provides a comprehensive review on the genetic variability of the RYMV, its epidemiology and control measures, and the gene action responsible for RYMV resistance.

The review also summarises complementary genomic tools useful in RYMV disease resistance breeding.

Successful breeding of rice for RYMV resistance depends on the availability of genes for stable resistance, knowledge of the genetics of the host and, the availability of efficient phenotyping and pathotyping methods, and understanding of the genes involved and their pattern of inheritance. Information presented in the review can serve as a reference guide for rice breeding emphasising RYMV resistance, high yields and farmers-preferred traits.     

Intra-specific DNA polymorphism in pineapple (<Emphasis Type="Italic">Ananas comosus</Emphasis> (L.) Merr.) assessed by AFLP markers

Pineapple (Ananas comosus (L.) Merr.) cultivars, often derived from somatic mutations, are propagated vegetatively. It has been suggested by isozyme data that there is little genetic variation among Smooth Cayenne cultivars. A thorough investigation of the genetic variation within the cultivated speciesAnanas comosus, particularly among commercial cultivars, will provide critical information needed for crop improvement and cultivar protection. One-hundred and forty-eight accessions ofA. comosus and 14 accessions of related species were evaluated with AFLP markers. The average genetic similarity ofA. comosus was 0.735 ranging from 0.549 to 0.972, suggesting a high degree of genetic variation within this species. With AFLP markers, discrete DNA fingerprints were detected for each commercial cultivar, breeding line, and intra-specific hybrid. Self-incompatibility, high levels of somatic mutation, and intraspecific hybridization may account for this high degree of variation. However, major cultivar groups of pineapple, such as Cayenne, Spanish, and Queen, could not be distinctively separated. These cultivar groups are based on morphological similarity, and the similar appearance can be caused by a few mutations that occurred on different genetic background. Our results suggest that there is abundant genetic variation within existing pineapple germplasm for selection, and discrete DNA fingerprinting patterns for commercial cultivars can be detected for cultivar protection. The genetic diversity and relationships of fourAnanas species are also discussed.     

Hevea gene pool for breeding

The conservation and utilization of allied gene resources is vital for the improvement of crop species. Rubber has been an undeniably beneficial commodity for the past 100 years. Progress in yield improvement over 70 years resulted in primary and hybrid clones with exceptional yielding abilities. The extension of Hevea to marginal areas necessitated breeding of new clones with resistance to environmental constraints. India, China, Brazil, Thailand, Côte d'Ivoire and Vietnam have marginal environments with single or multiple constraints such as low temperature, wind, higher altitude, moisture deficit and diseases. Allied species and accessions from the Brazil Amazonia can be integrated into such breeding programmes. Many of these clones are resultant of natural interspecific hybridizations. Also, allied species are excellent resources of timber. Molecular interventions revealed mtDNA of modern clones are highly conserved contributed by only two clones (PB 56 and Tjir 1). Nuclear DNA is highly divergent due to breeding and selection under varied geo-climates. The adaptation of allied species and wild accessions under a wide range of environments of Brazil is promising as a source of variation for breeding, and enables selection of clones for specific marginal areas.     

Potential of wild species for genetic enhancement of some semi-arid food crops

Discovery and incorporation of genes from wild species provide means to sustain crop improvement, particularly when levels of resistance in the cultigens are low and virulent strains of pests and pathogens overcome the host plant resistance. The extent of utilization and the potential of the wild genepool for genetic enhancement were reviewed in five important food crops viz. sorghum, pearl millet, chickpea, pigeonpea and groundnut grown in the semi-arid tropics. Introgression from compatible wild germplasm in the primary gene pool resulted in transfer of new cytoplasmic male sterility systems in pearl millet and pigeonpea, development of high protein, cleistogamous flower and dwarf pigeonpea lines and foliar disease resistant groundnut cultivars. Utilization of wild species in secondary and tertiary gene pools has been generally limited due to sterility, restricted recombination or cross incompatibility. Nevertheless, these species are extremely important as they contain high levels of resistance to several important biotic and abiotic stresses. Several of them, like those belonging to the Parasorghum section and the rhizomatous Arachis species are sources of multiple resistances and hold great promise to sustain crop productivity.     

利用GGE双标图和综合选择指数划分棉花品种生态区

为提高农作物品种多性状选育和应用的可靠性,本研究基于品种选择指数,应用GGE双标图进行了棉花品种生态区划分。首先依据国家棉花品种审定标准构建通用性强的品种选择指数(SI),即SI=0.40×皮棉产量+0.13×纤维比强度+0.09×(纤维长度+马克隆值)+0.11×枯萎病+0.09×黄萎病+0.10×霜前花率。然后,采用GGE双标图方法对2000—2013年期间39组(含585个单点试验)长江流域国家棉花区域试验中品种选择指数的基因型与环境互作效应及环境间关系进行综合评价与分析。研究结果将长江流域棉区划分为四川盆地生态区、南襄盆地生态区、浙江省沿海生态区和长江中下游生态区。其中,长江中下游生态区为长江流域的主要品种生态区,对长江流域的总体环境代表性最强,涵盖了湖南省环洞庭湖棉区、湖北省江汉平原和鄂东南岗地棉区、江西省环鄱阳湖棉区、安徽省沿江棉区、江苏省宁镇丘陵及沿江和沿海棉区;四川盆地生态区、南襄盆地生态区和浙江省沿海生态区均为特殊生态环境条件下的品种生态区,对总体环境代表性较差。因此,将以长江流域棉区为广谱适应性育种目标环境的棉花品种综合性状选择试验优先安排在长江中下游生态区中,有利于提高育种的总体选择效果,而其余品种生态区不适宜作为以长江流域为目标环境的品种综合性状选择环境,可侧重于特殊适应性品种选育。本研究充分展示了GGE双标图在品种生态区划分方面的应用效果,合理划分了长江流域基于选择指数的棉花品种生态区,可为长江流域棉区的品种多性状选择和推荐策略提供决策依据,也为其他棉区和作物品种生态区划分提供参考。     

Treasuring crop wild relative diversity: analysis of success from the seed collecting phase of the ‘Adapting Agriculture to Climate Change’ project

The seed collecting phase of the ‘Adapting Agriculture to Climate Change’ project was, to the best of our knowledge, the most comprehensive crop wild relatives (CWR) collecting and conservation mission to-date and provides priceless genetic diversity for ongoing and future crop breeding efforts. The seed collecting started in 2013 and was concluded in 2019, it was carried out in 22 countries in Africa, Asia, the Americas and Europe, involving CWR taxa of 28 different crop genepools. 3002 target seed accessions of 242 taxa were collected and are currently stored long-term in the countries of collection and, in most of the cases, backed up at the Millennium Seed Bank (UK). Considering also non-target species, 3854 seed accessions were collected. For the genepools of bambara groundnut (Vigna subterranea (L.) Verdc.), barley (Hordeum L.), grass pea (Lathyrus sativus L.), sorghum (Sorghum bicolor (L.) Moench), and wheat (Triticum L.), the collecting phase was highly successful in terms of diversity of both, species and populations. Despite the overall success of the project, in our analysis we discovered several issues that were encountered in the seed collecting. In particular, comparing the initial collecting targets with the seed accessions effectively collected it emerges that: (1) some important crop genepools were characterized by a low collecting success (e.g. banana/plantain (Musa L.), potato (Solanum tuberosum L.), rice (Oryza L.), (2) genepool 1 (the most important for breeding efforts) of some crop genepools was under-collected (e.g. eggplant (Solanum L.) and sorghum), (3) some important centres of plant biodiversity (especially the Indian Subcontinent) were underrepresented in the seed collecting. This analysis can guide further collecting missions in order to fill gaps in the long-term conservation of CWR of great importance for crop improvement.

     

Effect of Incorporation of Crop Residues on a Maize–Groundnut Sequence in the Humid Tropics. II. Soil Physical and Chemical Properties

Abstract

A two‐year study (1997–1999) was conducted on a sandy clay loam (Typic Paleudult) at the experimental farm of the Universiti Putra to determine the effects of application of crop residues on changes of some soil properties in a maize (Zea mays L.)–groundnut (Arachis hypogaea) crop rotation system. Five crops of a rotation of sweet corn–groundnut–sweet corn–groundnut–sweet corn were sown with three treatments: recommended inorganic fertilizer [nitrogen (N), phosphorus (P), and potassium (K)] with crop residue (T1), recommended inorganic fertilizer without crop residues (T2) or one‐half of the recommended inorganic fertilizer with crop residues combined with 10 t ha^?1 of chicken manure (T3). Soil organic carbon (OC), soil water content and soil bulk density were not significantly changed. Application of crop residues for two years increased cation exchange capacity (CEC) whereas supplementing crop residues with CM had significantly increased soil pH of the topsoil. Phosphorous in manure treatment had moved down the soil profile, which might cause eutriphication of under ground water, particularly during the rainy season. Based on this work, incorporation of crop residues could be a beneficial practice for improving the fertility of acid soils.     

Microsatellites based marker molecular analysis of Ghanaian bambara groundnut (Vigna subterranea (L.) Verdc.) landraces alongside morphological characterization

Bambara groundnut an indigenous crop of African origin is drought tolerant and the third most important leguminous crop in Ghana and Sub-Saharan Africa. In order to assess the level of genetic diversity within a small collection of Ghanaian landraces, molecular analysis was performed using microsatellite markers alongside characterization of morphological features. Genetic distance based on Jaccard’s similarity coefficient from the SSR marker analysis ranged from 0.48 to 0.9 among the landraces. 80 individual genotypes were clustered into 17 units with substantial levels of inter- and intra-landrace polymorphism. The analyses of variance from the morphological characterization for all quantitative traits were statistically significant (p < 0.05) except for terminal leaflet width. The first 4 principal components accounted for 41.97, 20.15, 13.39 and 9.81 % respectively of the morphological variations among the landraces. Qualitative traits however accounted for less of these variations. The results of the present study support the availability of high level of polymorphism within the collection of bambara groundnut analysed. This report is useful to crop improvement and germplasm conservation of bambara groundnut in Ghana.     

Selection criteria for grain yield and stability in bambara groundnut (Vigna subterranean (L) Verdc) landraces

The potential of bambara groundnut as a crop-based approach for the sustainable reduction of protein–energy malnutrition prevalent in Nigeria is still being explored. However, one of the limitations to sustainable production of this adapted species is low and unstable yield. Here, we employed multiple statistical analyses to determine traits that could be useful in predicting grain yield. Furthermore, additive main effect and multiplicative interaction and genotype × genotype × environment models were used to identify high yielding and stable landraces. Twenty-four bambara landraces were evaluated in two contrasting dry land growing seasons at four environments. Based on the results of correlation, path coefficient values and stepwise multiple regression analysis, it is reasonable to assume that seed growth rate would be effective as indirect selection criteria for grain yield improvement in this set of breeding materials under early and late planting environment. However, optimizing biomass growth rate, pod fill period, 100-seed weight, number of pods per plant and time to flowering may have important role in the improvement of grain yield in bambara groundnut. Due consideration should be given to 100-seed weight and time to flowering in the early dry and late planting environment. The possibility of successful cultivation of bambara groundnut in forest–savannah transition agricultural zone of Nigeria, particularly when planting is done around early August has been established in this study. However, based on the strong association between seed yield and its related characters in early and late planting environments, selection for higher seed growth rate combined with large number of pods appears to be the best indirect traits when selecting bambara groundnut plants to enhance grain yield under early and late planting environments. While landraces TVSu 1520 and 1578 were considered the best adapted landraces, TVSu 1670 and 1518 are promising landraces that could contribute to increasing grain yield stability.     

Assessment of farmers’ perceptions of production constraints,and their trait preferences of sorghum in western Ethiopia: implications for anthracnose resistance breeding

Sorghum, Sorghum bicolor (L.) Moench is an important food security crop widely grown by smallholder farmers in sub-Saharan Africa (SSA), including Ethiopia. In SSA, the potential of sorghum production and productivity has not been realised due to an array of constraints. Colletotrichum sublineolum disease is one of the main biotic constraints causing significant yield losses. The objectives of this study were to assess farmers’ perception, preferences and constraints to sorghum production and productivity in western Ethiopia, and to identify key drivers for anthracnose resistance breeding. A participatory rural appraisal study was undertaken in six selected districts in the East Wellega and West Shewa Administrative Zones in Ethiopia. Data were collected through structured questionnaires involving 165 respondent farmers. Further focus group discussions were held with 180 farmers and development agents. Sorghum is the third most preferred cereal crop after Eragrostis tef and Zea mays in western Ethiopia. About 79% of interviewed farmers cultivated sorghum during the study season. Farmers perceived that sorghum production is constrained by anthracnose disease, bird attack, loose smut and covered smut diseases. The most important farmer-preferred traits in sorghum varieties in the study areas were anthracnose resistance and tolerance to bird attack. Breeding sorghum varieties with the farmer-preferred traits is an important consideration to enhance productivity and adoption of improved sorghum cultivars in western Ethiopia.     

The importance of Guizotia abyssinica (niger) for sustainable food security in Ethiopia

Niger (noug; Guizotia abyssinica) is an economically important edible oilseed crop. This review sought to demonstrate the significance of niger for sustainable food security in Ethiopia, where it is produced exclusively by smallholders. In addition to its edible oil, niger seed is an important source of proteins, carbohydrates, vitamins and fiber that significantly contribute to the human diet. The crop has a wide genetic basis that is reflected in the form of a high variation in desirable traits, including seed yield, seed oil content, seed oil quality and photoperiod sensitivity. However, the wealth of niger genetic diversity has so far remained largely unexploited and research efforts have not yet yielded satisfactory results in the form of new and superior cultivars. The recent molecular and nutritional quality studies coupled with pre-breeding work have opened up new opportunities for the improvement of niger. A high yielding niger cultivars with oil content of up to 60 % and/or oleic acid content of up to 70 % can easily be bred based on Ethiopian niger gene pool through the combined use of novel genomic tools, traditional breeding and farmer-participatory approaches. The improvement of niger will have a significant contribution towards Ethiopia’s food security and sustainable development in general and self-sufficiency in edible oil in particular. Overall, an investment in the niger improvement programs will likely be of benefit far beyond Ethiopia’s borders and could potentially lead to the expansion of the crop outside the regions where it is currently grown.     

Bambara groundnut (Vigna subterranea) seed quality in response to water stress on maternal plants

Farmers who still cultivate bambara groundnut (Vigna subterranea) rely on landraces and seed retained from previous harvests. Given that the crop is typically cultivated in semi-arid regions, seed quality of farmers' retained seed might be compromised due to water stress experienced by maternal plants during production. The aim of this study was to determine the effect of water stress on maternal plants on subsequent seed quality of bambara groundnut. A single bambara groundnut landrace was characterised into four distinct selections based on seed coat and speckling colour. Initial seed quality (viability and vigour) was evaluated prior to planting seed in a field trial under irrigated and rainfed conditions. Final yield and yield components were determined at harvest. Thereafter, seed quality (viability and vigour) of progeny of different landrace selections was evaluated. Yield was lower under rainfed than irrigated conditions. Overall, subsequent seed quality showed improvement from initial seed quality of the original seedlot. Seed viability was higher in seeds produced under irrigated than rainfed conditions. Seed quality of bambara groundnut may be reduced underwater-limited production conditions. Seed enhancement practices such as priming may assist farmers to achieve better emergence. In the long term, seed production should be done under optimum conditions in order to achieve high-seed quality.     

A study of genetic diversity of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) in Vietnam and Cambodia estimated by RAPD markers

Sesame (Sesamum indicum L.) is a traditional oil crop cultivated throughout South East Asia. To estimate the genetic diversity of this crop in parts at the region, 22 sesame accessions collected in Vietnam and Cambodia were analyzed using 10 RAPD markers. The 10 primers generated 107 amplification products of which 88 were polymorphic fragments (83%). Genetic diversity of all populations was H_t = 0.34 when estimated by Nei’s genetic diversity and species diversity was H′_sp = 0.513 when estimated by Shannon diversity index. Genetic distance ranged from 0.03 to 0.43, with a mean genetic distance of 0.23. The unweighted pair group method with arithmetic averages (UPGMA) cluster analysis for the 22 accessions divided the material in four groups. The dendrogram revealed a clear division among the sesame accessions based on their geographical region. Interestingly, some geographically distant accessions clustered in the same group, which might indicate the human factor involved in the spreading of sesame varieties. The high level of polymorphism shown suggests that RAPD techniques can also be useful for the selection of parents in sesame (Sesamum indicum L.) breeding program and for cultivar differentiation.     

Effects of Cultivars,Organic Cropping Management,and Environment on Antioxidants in Whole Grain Rice

Whole grain rice contains functional antioxidants such as phenolics, flavonoids (including proanthocyanidins), vitamin E homologs (tocopherols and tocotrienols), and γ‐oryzanol that have positive effects on human health. These antioxidants are secondary metabolites in plants that can be induced under external stress. The objectives of this study were to quantify the effects of cultivars, crop management method (organic and conventional), and growing environment on the concentrations of these antioxidants in whole grain rice. Cultivars and environment contributed to a higher percentage of variation in the concentrations of these antioxidants than did crop management method. Cultivars accounted for a greater proportion of the variation than environment for all traits except total tocotrienols and γ‐oryzanol. Cultivars that are high in concentrations of these antioxidants were identified, but no one cultivar contained the highest concentration of all antioxidants evaluated. These cultivar differences indicate that improvement for phytochemical and antioxidant traits can be accomplished through traditional breeding. Because of the limited effect of crop management on these antioxidants, choice of cultivar should be the focus for organic production of whole grain rice high in these antioxidants.     

Variation in a wild groundnut species, Arachis duranensis Krapov. & W.C. Gregory

Forty-two accessions of Arachis duranensis, a wild groundnut species that has been reported as a source of resistance to several groundnut diseases, were studied for 30 quantitative traits including total protein content, oil content, and reaction to groundnut rust. Protein profiles were also investigated for variation at the molecular level. Principal component analysis was applied to 28 traits that showed significant variation. Of these, only five characters, namely, height of the main stem, length of apical leaflet on the main stem, length of isthmus between pods, width of seed, and reaction to groundnut rust, accounted for more than 61.4% of the total variation. Protein profiles of these accessions were broadly similar, except some accessions which differed in few bands. The importance of these variations in strategies for germplasm collection and breeding is discussed.Submitted as Journal Article No. 1507 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru P.O. 502 324 A.P. India.     

分子标记辅助选择在作物育种中的应用及展望

分子标记辅助选择(Marker-assisted-selection；MAS)是作物遗传改良的有效工具。随着高通量低成本SNP标记的开发应用和生物信息学的快速发展，MAS的应用拓展到了全基因组选择(Genomic Selection，GS)，大大地提高了选择的效率和精准性。因技术和费用的限制，MAS未能广泛应用。为拓展MAS在作物育种中的应用路径，并发挥其最大潜力。通过查阅相关文献，综述了MAS在作物育种中的优势及其应用途径；分析了MAS应用受限的原因所在，并针对具体问题提出了对策；预测了MAS的应用前景:因高通量基因分型及基因组测序技术等的快速发展，未来MAS费用肯定显著降低，选择效率将大幅提升，致使MAS的应用空间更为广阔。     

A short review on sugarcane: its domestication,molecular manipulations and future perspectives

Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.

     

Dry Matter,Nitrogen, Phosphorous,and Potassium Partitioning,Accumulation, and Use Efficiency in Transgenic Cotton-Based Cropping Systems

A better understanding of the fate of nutrients in transgenic cotton (Gossypium hirsutum L.) fields will improve nutrient efficiencies, will optimize crop growth and development, and may help to enhance soil quality. A study was made to evaluate and quantify the effect of cropping system [sole cotton and groundnut (Arachis hypogaea) intercropping with transgenic cotton] and nitrogen (N) management [control (0N), 100% recommended dose of nitrogen (RDN) through urea, substitution of 25% RDN through farmyard manure (FYM), and substitution of 50% RDN through FYM] on dry matter (DM) and nutrient partitioning and accumulation by transgenic cotton and groundnut at New Delhi during 2006–2007. Soil and plant samples were collected and analyzed at 60, 90, and 120 days after sowing and at harvest. Results revealed that intercropping of groundnut with cotton did not significantly affect DM and nutrient partitioning in cotton, but residual soil fertility in terms of potassium permanganate (KMnO₄) N showed an improvement in contrast to Olsen's P and ammonium acetate (NH₄OAc)–exchangeable K over sole cotton. At harvest, of total DM assimilated, leaves constituted 10–20%, stem 50%, and reproductive parts of cotton accounted for the rest. For each kilogram of seed cotton produced, the crop assimilated 61 g of N, of which 23 g was partitioned to harvested seed cotton. Substitution of 25% RDN through FYM, being on par with 100% RDN through urea, recorded greater DM, nutrient uptake in different parts of cotton, agronomic N-use efficiency (9.5 kg seed cotton kg N^?1), and apparent N recovery (83.3%) over 50% RDN substitution through FYM and control. The control, being on par with 50% RDN substitution through FYM, recorded significantly greater DM and nutrient uptake by intercropped groundnut over other treatments. Apparent N and potassium (K) balance at the end of study was negative in all treatments; however, the actual change in KMnO₄ N was positive in all the treatments except control. Our study suggests that intercropping of groundnut with transgenic cotton and substitution of 25% dose of N through FYM is sustainable in tropical countries.