Genomics,genetics and breeding of tropical legumes for better livelihoods of smallholder farmers

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP‐GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large‐scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega‐initiatives facilitated release of a number of new varieties and also dissemination of on‐the‐shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics‐assisted breeding approaches and rapid generation advancement.     

Farmer and formal breeding of sorghum (Sorghum bicolor (L.) Moench) and the implications for integrated plant breeding

Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop worldwide and it is the fourth most important crop in Ethiopia. The national average yield amounts 1302 kg/ha. In order to assess the achievement in farmer breeding various types of research were undertaken. These include survey research to quantify the trend in productivity, the level of and reasons for adoption of improved varieties, yield performance and preference evaluation of farmers’ varieties (FVs) and improved varieties (IVs). As per the trend analysis over the last four decades, total production and yield per hectare has increased by 11.63 and 14.2%, respectively. However, area allocated to sorghum has decreased over years by −2.93%. The lack of consistent productivity is attributed to the fluctuation of environmental factors. Sorghum production in Ethiopia is predominantly based on varieties developed by farmers. The share of IVs is very low. FVs and IVs are adopted by 87.3 and 12.7% of the farmers, respectively. Besides, the adoption of IVs is limited to the lowland crop ecology. The comparative yield of FVs is higher than IVs by 132%. On top of yield, farmers do prefer their varieties for other multipurpose values namely feed, fuel wood and construction material. FVs under production are identified in each wereda. Farmer breeding has been successful compared to four decades of formal breeding. On the other hand, both farmer and formal breeding are not without weaknesses; a comparative balance sheet is outlined for both. Ideotypes for the three major crop ecologies are suggested and integrated plant breeding is anticipated to develop the proposed ideotypes thereby increase sorghum productivity in the region.     

Biotechnology approaches to overcome biotic and abiotic stress constraints in legumes

Summary Biotic and abiotic stresses cause significant yield losses in legumes and can significantly affect their productivity. Biotechnology tools such as marker-assisted breeding, tissue culture, in vitro mutagenesis and genetic transformation can contribute to solve or reduce some of these constraints. However, only limited success has been achieved so far. The emergence of “omic” technologies and the establishment of model legume plants such as Medicago truncatula and Lotus japonicus are promising strategies for understanding the molecular genetic basis of stress resistance, which is an important bottleneck for molecular breeding. Understanding the mechanisms that regulate the expression of stress-related genes is a fundamental issue in plant biology and will be necessary for the genetic improvement of legumes. In this review, we describe the current status of biotechnology approaches in relation to biotic and abiotic stresses in legumes and how these useful tools could be used to improve resistance to important constraints affecting legume crops.     

Wheat breeding for end-product use

High grain yield is the primary objective of most wheat breeding programs around the world. In some countries, for example Australia and Canada, a new wheat cultivar must meet a prescribed level of quality before it can be registered for commercial production. For most traditional uses, wheat quality derives mainly from two interrelated characteristics: grain hardness and protein content. Grain hardness is a heritable trait but it can be strongly affected by abnormal weather conditions such as excessive rainfall during the harvest period. Protein content is weakly heritable and strongly dependent on environmental factors such as available soil nitrogen and moisture during the growing season. In addition, each end-use requires a specific 'quality' in the protein. Quality is determined by the molecular structure of the major proteins of flour which, in turn, controls the interactions of the proteins during the breadmaking process. Durum wheats have the hardest grain texture and are usually high in protein content. They are especially suited to the production of pasta because of their highly vitreous grain (high milling yield of semolina), unique combination of storage proteins for good cooking quality of pasta, and high yellow pigment content required for attractive appearance of cooked product. All three characteristics are highly heritable and can be readily improved by conventional breeding. Recent research has shown that the presence of γ-gliadin 45 is a reliable marker of good cooking quality. This marker is now used for screening early generation material in many durum wheat breeding programs. Common (hexaploid) wheats cover a wide range of grain hardness and protein content. The hardest wheats of this class, generally highest in protein, are used for pan bread. Considerable progress has been achieved in research of the molecular properties of flour proteins that are required for highest bread quality. The key protein component in this regard is glutenin. Segregating breeding populations can be screened by electrophoresis or high performance liquid chromatography for the presence of desirable glutenin subunits. Common wheats of medium hardness and lower protein content are used for other types of bread and noodles. Wheats with softest texture and lowest protein are used for cakes and cookies. In some end-uses, e.g., Chinese-type noodles, starch quality is important together with protein quality; this feature should be taken into consideration in developing a screening strategy for wheats for this application. Screening tests that reflect end-use requirements for most of the known products are available, and should be applied in testing wheats according to intended use. This revised version was published online in August 2006 with corrections to the Cover Date.     

Lathyrus improvement for resistance against biotic and abiotic stresses: From classical breeding to marker assisted selection

Summary Several Lathyrus species and in particular Lathyrus sativus (grass pea) have great agronomic potential as grain and forage legume, especially in drought conditions. Grass pea is rightly considered as one of the most promising sources of calories and protein for the vast and expanding populations of drought-prone and marginal areas of Asia and Africa. It is virtually the only species that can yield high protein food and feed under these conditions. It is superior in yield, protein value, nitrogen fixation, and drought, flood and salinity tolerance than other legume crops. Lathyrus species have a considerable potential in crop rotation, improving soil physical conditions; reducing the amount of disease and weed populations, with the overall reduction of production costs. Grass pea was already in use in Neolithic times, and presently is considered as a model crop for sustainable agriculture. As a result of the little breeding effort invested in it compared to other legumes, grass pea cultivation has shown a regressive pattern in many areas in recent decades. This is due to variable yield caused by sensitivity to diseases and stress factors and above all, to the presence of the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), increasing the danger of genetic erosion. However, both L. sativus and L. cicera are gaining interest as grain legume crops in Mediterranean-type environments and production is increasing in Ethiopia, China, Australia and several European countries. This paper reviews research work on Lathyrus breeding focusing mainly on biotic and abiotic resistance improvement, and lists current developments in biotechnologies to identify challenges for Lathyrus improvement in the future.     

Demand-driven breeding of food legumes for plant-nutrient relations in the tropics and the sub-tropics: serving the farmers; not the crops!

A number of improved cultivars of food legume crops have been developed and released in the tropics and the sub-tropics. Most of these cultivars have been developed through conventional breeding approaches based on the development of crop varieties under optimum soil fertility levels. Nevertheless, it is hardly possible to say that the varietal provisions made by the past approach have been readily accepted, and properly utilized to boost productivity of food legumes grown by resource-poor farmers. The approach itself did not fully appreciate the actual circumstances of the resource-poor farmers where marginal production systems prevail and the poorest farmers could not afford to use cultivars developed under optimum soil fertility level. Therefore, the limitations and strategic implications of past experiences made to develop crop cultivars need to be analyzed in order to formulate better strategies and approaches in the future. The main purpose of this article is to review the efforts made, the technical difficulties associated with the genetic improvement in food legumes as related to plant-nutrient relations, causes of limited breeding success and thereby draw lessons useful to designing future breeding strategies. The scope of nutrient deficiency stress and the approaches to breeding for plant-nutrient relations are discussed and the need for refining the approach and better targeting of the breeding methodologies suggested.     

Genetics,genomics and breeding of groundnut (Arachis hypogaea L.)

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker‐assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.     

Drought Stress in Grain Legumes during Reproduction and Grain Filling

Water scarcity is a major constraint limiting grain legume production particularly in the arid and semi‐arid tropics. Different climate models have predicted changes in rainfall distribution and frequent drought spells for the future. Although drought impedes the productivity of grain legumes at all growth stages, its occurrence during reproductive and grain development stages (terminal drought) is more critical and usually results in significant loss in grain yield. However, the extent of yield loss depends on the duration and intensity of the stress. A reduction in the rate of net photosynthesis, and poor grain set and grain development are the principal reasons for terminal drought‐induced loss in grain yield. Insight into the impact and resistance mechanism of terminal drought is required for effective crop improvement programmes aiming to improve resistance to terminal drought in grain legumes. In this article, the impact of terminal drought on leaf development and senescence, light harvesting and carbon fixation, and grain development and grain composition is discussed. The mechanisms of resistance, management options, and innovative breeding and functional genomics strategies to improve resistance to terminal drought in grain legumes are also discussed.     

Phenotypic evaluation of floral and flowering traits with relevance for hybrid breeding in wheat (Triticum aestivum L.)

Hybrid breeding is a promising approach to increase the yield potential in wheat (Triticum aestivum L.). The profitability of wheat hybrids highly depends on a cost‐efficient system for hybrid seed production for which an adequate outcrossing in the male pool is of utmost importance. Employing a set of 51 elite winter wheat lines, we developed and evaluated phenotyping methods for floral and flowering traits with relevance for improved cross‐pollination. We observed significant genotypic variances and high heritabilities for most traits, including important traits like pollen mass and anther extrusion. Our results suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross‐fertilization.     

Conditions favouring doubled haploid breeding over conventional breeding of self-fertilizing crops

Summary Monte Carlo computer simulation was used to investigate the conditions favouring doubled haploid breeding over conventional breeding of self-fertilizing crops. Two different systems of doubled haploid breeding and three systems of conventional breeding were compared for two criterion parameters, i.e., the probability of obtaining desirable genotypes and the expected genetic advance of selected lines. It was inferred that the efficiency of production of haploid and doubled haploid plants primarily determines the success of the doubled haploid breeding method. In doubled haploid breeding, about 1/5, hopefully 1/2 as many test plants need to be raised as in conventional breeding to achieve the same level of success. With this condition begin satisfied, the doubled haploid breeding method can efficiently be used when one or more of the following conditions are met: (i) a relatively small number of loci, presumably ten of less, is involved with the breeding objective concerned, (ii) desirable alleles are recessive to undesirable ones at most, if not all, of the segregating loci, and (iii) the genes are not strongly linked. It was confirmed that the doubling of haploids can better be applied to selected F₂ plants rather than to F₁ plants.     

Plant breeding: past,present and future

Plant breeders can help farmers increase food production by breeding new cultivars better adapted to their chosen farming systems, but these must be capable of providing the necessary plant inputs for the required levels of crop production in 2050. Until 200 years ago the farmers themselves were the plant selectors. Plant domestications, extensive crop dispersions and farmers’ selections produced thousands of locally adapted landraces of cultivated plants. During the twentieth century these were largely replaced by relatively few high yielding cultivars and the natural habitats of many of their wild relatives became endangered. Hence in situ and ex situ conservation, and evaluation and use of plant genetic resources is vital for future plant breeding. The development of scientific breeding from the beginning of the twentieth century was based on understanding the mechanism of inheritance and the mating systems of crop plants. The types of genetically uniform, high yielding cultivars that have been bred from genetically heterogeneous landraces were determined by the mode of reproduction and mating system of the cultivated plant species: inbred line (wheat) and hybrid (rice) cultivars for inbreeding species, hybrid (maize) cultivars for outbreeding species, and clonal (potato) cultivars for vegetatively propagated species. When genetically heterogeneous crops are desired, mixtures of cultivars and synthetic cultivars can be produced. Future progress in crop improvement will come from three complementary approaches: use of hybridization and selection in further conventional breeding, base broadening and introgression; mutation breeding, cisgenesis and gene editing; and genetically modified crops.     

Variance component estimations and allocation of resources for breeding sweetpotato under East African conditions

In Africa, average sweetpotato storage root yields are low and breeding is considered to be an important factor in increasing production. The objectives of this study were to obtain variance component estimations for sweetpotato in this region of the world and then use these to determine the efficiency of variety trials and breeding systems. From an incomplete series of variety trials in Kenya and Uganda (comprising 15 genotypes, three locations, two crop durations and three seasons) variance components were estimated ‐ using the REML method ‐ for the following traits: storage root yield, biomass production, harvest index, storage root dry matter and the Elston index which was used to aggregate all four traits. The storage root yield of clones across all 12 environments ranged from 15.2 to 33.0 t/ha. The variance components were significant for all traits, except the genotype by season interactions for storage root dry matter. The efficiency of selection systems was determined for total test capacities of 450 and 900 plots and using not more than five locations. Two‐stage selection was 17‐81% more efficient than one‐stage selection after two seasons of testing. Two‐stage selection was optimized under the restriction of using at least two locations at step 1. Trials with two locations and one replication at step 1 and five locations and two replications at step 2 were appropriate both for selecting for storage root yield and for simultaneously selecting for storage root yield, biomass production, harvest index and storage root dry matter content by using the Elston index. There are indications that such an allocation of resources for breeding sweetpotato is also appropriate for other regions in Sub‐Saharan Africa.     

The twenty-first century,the century of plant breeding

To achieve global food security by 2050 primary production must almost be doubled, at least to 80 % by increasing production per unit land. The challenge to plant breeding is tremendous. It is necessary to convince the public of this challenge, who are already dealing with concerns about climate change, a scarcity of good arable land, the demands placed on land with regard to biomass production, scarcity of water and phosphorous as well as increasing consumption of meat. In terms of breeding, concerns are the very small number of major crops and low rates of breeding progress in self-pollinating cereals. Society and politicians can be easily distracted from the dire need to invest in basic breeding research and breeding applications when so many environmental concerns are being emphasized. A holistic approach to these problems is essential. The focus here is on both the obstacles to be overcome and the opportunities to ensure global food security by producing excellent germplasm by 2050. This can be achieved by new technologies and genomics as well as the continuing development of more traditional breeding methodologies.     

Choice of shrinkage parameter and prediction of genomic breeding values in elite maize breeding populations

Genomic selection (GS) is a promising alternative to marker‐assisted selection particularly for quantitative traits. In this study, we examined the prediction accuracy of genomic breeding values by using ridge regression best linear unbiased prediction in combination with fivefold cross‐validation based on empirical data of a commercial maize breeding programme. The empirical data is composed of 930 testcross progenies derived from 11 segregating families evaluated at six environments for grain yield and grain moisture. Accuracy to predict genomic breeding values was affected by the choice of the shrinkage parameter λ², by unbalanced family size, by size of the training population and to a lower extent by the number of markers. Accuracy of genomic breeding values was high suggesting that the selection gain can be improved implementing GS in elite maize breeding programmes.     

Functional male sterility (ps-2) in tomato (Lycopesicon esculentum Mill.) and its application in breeding and hybrid seed production

Data and findings concerning the development of an effective male sterility system (as already applied in the practice of producing tomato hybrid seed) through the use of the positional sterility (ps 2) gene are reported. Undesirable selfing and the necessity of emasculation are discussed as the two main disadvantages that limit the use of ps 2-sterile seed parents in tomato hybrid seed production. The following specific characteristics in the performance of ps 2-lines were evaluated: 1) the percentage of selfing in the ps 2-lines varies within and between the years of growing, being forever lowest during the period of hybrid seed production; 2) the percentage of selfed seeds when using a ps 2-line as seed parent in producing hybrid seed is significantly lower than the percentage of selfing, observed on this same line; 3) the ps 2-gene expressivity varies depending on the genotype. This enables the breeding of ps 2-lines exhibiting very low percentage of selfing; 4) stamen emasculation at anthesis (as applied in ps 2-lines) is significantly easier and more rapid than emasculation in floral buds. The easy maintenance of the sterile lines – by artificial selfing it is possible to produce 100% ps 2 progeny – and the high yield of hybrid seed obtained are discussed as important advantages in using this type of sterility in tomato hybrid seed production. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetics and biology of cytoplasmic male sterility and its applications in forage and turf grass breeding

Hybrid breeding can exploit heterosis and thus offers opportunities to maximize yield, quality and resistance traits in crop species. Cytoplasmic male sterility (CMS) is a widely applied tool for efficient hybrid seed production. Encoded in the mitochondrial genome, CMS is maternally inherited, and thus, it can be challenging to apply in breeding schemes of allogamous self‐incompatible plant species, such as perennial ryegrass. Starting with a general introduction to the origin and the function of mitochondria in plants, this review focuses on the genetics and biology of CMS systems in plants to identify conserved and system‐specific mechanisms. We examine prospects of comparative mitochondrial genomics to identify candidate genes and causative polymorphisms associated with CMS across species and discuss specificities, obstacles and potentials of CMS as a breeding tool for maximizing heterosis in forage grasses. The purpose of the review is to highlight the importance of CMS and hybrid breeding in grasses, with the aim of facilitating research and development of novel breeding strategies to address the future needs for food, feed and biomass production.     

Modified synthetic varieties: a breeding method for forage crops to exploit specific combining ability

Hybrid varieties have not become commercially successful in perennial and self‐incompatible forage crops because of their severe inbreeding depression and/or ineffectiveness in commercial seed production. Here, a modified synthetic variety (MSV), a breeding method for forage crops is proposed, where specific combining ability (SCA) is exploited in a way different from that in hybrids. As Syn‐l seeds from only two of its parental clones are used to produce its Syn‐2, its performance in Syn‐2 partially depends on the SCA between the two seed parents. The inbreeding coefficient of MSVs can be as low as that of conventional synthetic varieties sold today. To evaluate its advantages, 15 modified synthetic strains (MSSs) of timothy were developed from a set of Syn‐l seeds of a conventional synthetic strain (CSS) having six parental clones. An MSS (Syn‐2) showed a yield level equivalent to and a disease score significantly lower than the CSS (Syn‐1) in a field test. The diallel crossing analysis implied that the SCA effects are influential for yield, and that MSV or other SCA‐exploiting breeding methods have the potential to improve the yield level of timothy effectively.     

Reciprocal effects in true potato seed breeding in short-day length environments

Reciprocal crosses may have significantly distinct performances regarding tuber characteristics in potato, suggesting the importance of cytoplasmic effects in this crop. The selection of parents for true potato seed breeding therefore needs to consider this potential effect when determining the direction of a cross. The aim of this research was to determine whether a broad‐based true potato seed breeding population, developed at the Centro Internacional de la Papa, could be affected by cytoplasmic effects in the short‐day length environments of the tropics. Two random sets of reciprocal biparental crosses were included in the first set of experiments, which were grown in two contrasting Peruvian locations. Only one out of 14 reciprocal crosses showed significantly distinct performance for tuber yield and tuber set. In the second set, only one of each of the 12 reciprocal crosses had distinct performance for vine earliness, days to flowering and flowering intensity, but four of the reciprocal crosses in the second set showed distinct pollen production. The results suggest that cytoplasmic effects in this breeding population are more important for reproductive characteristics such as pollen production than for tuber yield. This finding is not surprising because male sterility in potato results from the interaction between sensitive cytoplasm and dominant nuclear genes.     

Participatory plant breeding with maize in Mexico and Honduras

Maize is a staple food crop in many developing countries. However, if seven major maize producing countries are excluded from this group, data indicate that only 34% of the maize area is planted with improved seed despite considerable effort invested in maize breeding. This has led researchers to investigate other options, such as farmer-participatory plant breeding, for delivering the benefits of plant breeding knowledge and technology to farmers in developing countries. This paper describes short-term results from participatory maize breeding studies in Mexico and Honduras. Results from three selection cycles in Mexico suggest that stratified mass selection without pollination control, with selections carried out by researchers in farmers' fields, may be effective at improving yield in farmers' local varieties. In Honduras, mass selection with pollination control, where selections were done by collaborating farmers in their own fields on their own varieties, showed trends (non-significant) towards yield improvement. Farmer selection seemed to offer the greatest yield benefit over experiment station selection on the farm with the lowest yield potential, suggesting that farmer-participatory approaches may be most advantageous in marginal environments where experiment station conditions differ most dramatically from farmers' conditions. These studies highlighted the importance of seed systems knowledge in designing participatory plant breeding programs. For cross-pollinated crops, they also highlighted the need to balance progress from selection and demands on farmers' time and labor in choosing breeding methods. Further work is needed to investigate farmer-participatory breeding approaches that can address post-harvest traits. This revised version was published online in August 2006 with corrections to the Cover Date.     

Resistance to insect pests: What do legumes have to offer?

Summary Insect pests are major problems for all crops, worldwide. In this review we will focus on legumes, which are attacked by a range of insect pests including pod/seed feeders, defoliators and sap feeders. We review the history of breeding for resistance to insect pests in legumes, which has had mixed success, and discuss further opportunities in this area. We also review the extraordinary array of direct and indirect mechanisms contributing to insect defence in legumes, the understanding and exploitation of which offer opportunities for both legume and non-legume crops. There is also good potential to improve insect resistance in legume crops through a detailed understanding of the signaling pathways that regulate induced responses to insect feeding, and recent progress in this area, primarily obtained from non-legume systems, is reviewed. The importance legumes play in farming systems, their wide range of novel chemistry and the emergence of model systems suitable for genomic approaches present opportunities for research in this area strongly linked to breeding programs to help develop legume crops with enhanced insect resistance. CSIRO’s right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged.