Enhancing onion breeding using molecular tools

Bulb onion (Allium cepa L.) is an ancient crop that is thought to have originated in Central Asia and has been cultivated for over 5000 years. Classical genetic and plant breeding approaches have been used to improve onion yield, quality, and resistance against biotic and abiotic stresses. However, its biennial life cycle, cross‐pollinated nature and high inbreeding depression have proved challenging for the characterization and breeding of improved traits. New technologies, notably next‐generation sequencing, are providing researchers with the genomic resources and approaches to overcome these challenges. Using these genomic technologies, molecular markers are being rapidly developed and utilized for germplasm analysis and mapping in onion. These new tools and knowledge are allowing the integration of molecular and conventional breeding to speed up onion improvement programmes. In this review, we outline recent progress in onion genomics and molecular genetics and prospects for enhancing onion yield and quality in the future.     

Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

Citrus breeding,genetics and genomics in Japan

Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering.     

Genetic Variations and Adaptations in Chickpea

A total of 329 chickpea lines, comprising 130 kabiili and 199 desi types, originating from six regions, viz., Indian sub-continent, Middle East, North Africa, America, Europe and USSR, were sown in augmented design. The data recorded on agronomic characters on all entries from each region were evaluated in terms of group (region) means. Among the six regions, greater plant height and lateness in flowering were specific to USSR entries. Group means of USSR accessions, both desi and kabuli, differed significantly from those of Indian varieties for a majority of the characters. These observations indicate that the degree of expression of certain characters could be ascribed to specific areas, which led to area-specific adaptations. Furthermore, type-specific differentiating characters, differing in degree of expression, were observed in desi and kabuli types. For example, high mean values of characters, like branches, pods, grain yield and harvest index, were associated with desi types, and 100-seed weight with kabulis. History of cultivation and selection for specific purpose has been cited as cause for area-specific adaptations and type-specific differentiating characters.     

Effect of Sulphur and Foliar-applied Chemicals on Cold Tolerance in Chickpea (Cicer arietinum L.)

In a field study it was observed that sulphur fertilization of chickpea at 100 kg S ha⁻¹ imparted cold tolerance under low temperature stress conditions. Further, foliar sprays of DMSO, H₂SO⁴, KCl and H³BO³ proved effective in alleviating cold injury. Glucose spray also showed efficacy in this regard. The effects of sulphur fertilization and foliar applied DMSO and H²SO⁴ were largely associated with improved sulphur nutrition of plants, while improvement in K content under KCl treatment and B content under H₃BO₃ treatment was responsible for cold tolerance effects. Improvement in overall soluble carbohydrate and protein status of plants was held responsible for glucose effects possibly associated with osmoregulation.     

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.     

Kazusa Marker DataBase: a database for genomics,genetics, and molecular breeding in plants

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.     

Cisgenesis and genome editing: combining concepts and efforts for a smarter use of genetic resources in crop breeding

Plant genetic resources (PGR) represent valuable sources of genetic variability for crop breeding. The development of novel biotechnologies is necessary for increasing the efficiency of their use in pre‐breeding and breeding work. The genome sequencing of hundreds of genotypes and the mining of allele diversity in major crops and populations of landraces and wild relatives allow the isolation of genes underlying characters of interest and their precise modification or transfer into targeted varieties. The technological developments and applications of new plant breeding techniques (NPBT) that maximize the similarity with gene transfer by crossing (cisgenesis/intragenesis) or the accuracy of biotechnological approaches (genome editing) are reviewed. Their potentialities and current limitations as well as the possible advantages of using them separately or combined for the exploitation of PGR in crop breeding are also discussed. Above‐mentioned NPBT tackle some objections to the application of biotechnologies in agriculture and are under review worldwide to assess the possible exclusion from the current regulation systems for genetically modified plants.     

Cold Stress Injury during the Pod-Filling Phase in Chickpea (Cicer arietinum L.): Effects on Quantitative and Qualitative Components of Seeds

Chilling stress (<10 °C) is detrimental for chickpea, especially at the reproductive phase and leads to abortion of flowers, pods and impaired seed filling, causing severe reduction in yield. The information on the effects of low temperature during different pod-filling stages on quality and quantity of developing seeds is lacking in chickpea and hence this study. In this study, chickpea plants growing under warm conditions of the glasshouse were subjected to cold conditions of the field at the two stages, (a) early pod-filling and (b) late pod-filling, and subsequently analysed for stress injury in terms of electrolyte leakage (EL), 2,3,5-triphenyl tetrazolium chloride reduction, relative leaf water content and total chlorophyll content in the leaves of control and cold-stressed plants. Cold stress caused elevation of EL but reduced all the other parameters. Sucrose content decreased significantly in the leaves of cold-stressed plants. The differences between the effects of stress at two stages on the total plant dry weight were small and insignificant. The seed growth rate, seed fill duration, seed number, and average seed weight and size decreased greatly in the plants cold-stressed at the late pod-filling stage than those stressed at the early pod-filling stage. Greater reduction was observed in starch, proteins, soluble sugars, fat, crude fibre and storage protein fractions in the seeds of the plants cold-stressed at the late pod-filling stage. This coincided with a larger decrease in sucrose content, the activities of sucrose synthase, invertase and starch synthase observed at this stage. The germination and growth potential were, however, inhibited to a greater extent in seeds of plants stressed at the early pod-filling stage.     

Heat stress in crop plants: its nature,impacts and integrated breeding strategies to improve heat tolerance

Increasing severity of high temperature worldwide presents an alarming threat to the humankind. As evident by massive yield losses in various food crops, the escalating adverse impacts of heat stress (HS) are putting the global food as well as nutritional security at great risk. Intrinsically, plants respond to high temperature stress by triggering a cascade of events and adapt by switching on numerous stress‐responsive genes. However, the complex and poorly understood mechanism of heat tolerance (HT), limited access to the precise phenotyping techniques, and above all, the substantial G × E effects offer major bottlenecks to the progress of breeding for improving HT. Therefore, focus should be given to assess the crop diversity, and targeting the adaptive/morpho‐physiological traits while making selections. Equally important is the rapid and precise introgression of the HT‐related gene(s)/QTLs to the heat‐susceptible cultivars to recover the genotypes with enhanced HT. Therefore, the progressive tailoring of the heat‐tolerant genotypes demands a rational integration of molecular breeding, functional genomics and transgenic technologies reinforced with the next‐generation phenomics facilities.     

Screening for resistance in the primary and secondary gene pool of barley against the root-lesion nematode Pratylenchus neglectus

Root-lesion nematodes of the genus Pratylenchus are significant pests in crop cultivation throughout many parts of the world. A study was initiated to determine the resistance of Hordeum vulgare and H. vulgare ssp. spontaneum (wild barley) against one major representative of the genus Pratylenchus , P. neglectus . A glasshouse test was first established. Barley seedlings were grown in 20 cm³ tubes filled with sand. Each plant was inoculated with 400 P. neglectus juveniles. After 12 weeks of cultivation nematodes were isolated from roots and sand using a misting chamber. The nematodes were counted under a microscope. A representative collection of 565 barley and wild barley accessions was tested in this way. The average number of nematodes per accession ranged from 350 to 12 000. In a verification experiment, 35 accessions with low and high infection rates were tested. This experiment identified a number of accessions with low infection rates. The perspectives for future breeding of barley cultivars resistant to root-lesion nematodes are discussed.     

Achievements and limitations of contemporary common bean breeding using conventional and molecular approaches

Common bean (Phaseolus vulgaris L.) improvement programs have been successful using conventional breeding methods to accomplish a wide array of important objectives. Specific achievements include the extension of range of adaptation of the crop, the development of cultivars with enhanced levels of disease and pest resistance and breeding lines that possess greater tolerance to drought. The most effective breeding method depends on the expression and inheritance of the trait to be selected and the target environment. Many bean improvement programs use molecular markers to facilitate cultivar development. In fact, several recent germplasm releases have used molecular markers to introgress and or pyramid major genes and QTL for disease resistance. Related species (P. coccineus and P. acultifolius) via interspecific hybridizations remain an important albeit long-term source for resistance to economically important diseases. Slow progress has been made in the improvement of traits such as adaptation to low soil fertility and tolerance to high levels of soluble Al in the soil using conventional breeding methods. The inability to directly measure root traits and the importance of genotype × environment interaction complicate the selection of these traits. In addition, symbiotic relationships with Rhizobium and mycorrhiza need to be taken into consideration when selecting for enhanced biological N fixation and greater or more efficient acquisition of soil P. Genomic examination of complex traits such as these should help bean breeders devise more effective selection strategies. As integration of genomics in plant breeding advances, the challenge will be to develop molecular tools that also benefit breeding programs in developing countries. Transgenic breeding methods for bean improvement are not well defined, nor efficient, as beans are recalcitrant to regeneration from cell cultures. Moreover, if issues related to consumer acceptance of GMOs cannot be resolved, traits such as herbicide tolerance in transgenic bean cultivars which would help farmers reduce production costs and decrease soil erosion will remain unrealized.     

Cowpea (Vigna unguiculata): Genetics,genomics and breeding

Cowpea, Vigna unguiculata (L.), is an important grain legume grown in the tropics where it constitutes a valuable source of protein in the diets of millions of people. Some abiotic and biotic stresses adversely affect its productivity. A review of the genetics, genomics and breeding of cowpea is presented in this article. Cowpea breeding programmes have studied intensively qualitative and quantitative genetics of the crop to better enhance its improvement. A number of initiatives including Tropical Legumes projects have contributed to the development of cowpea genomic resources. Recent progress in the development of consensus genetic map containing 37,372 SNPs mapped to 3,280 bins will strengthen cowpea trait discovery pipeline. Several informative markers associated with quantitative trait loci (QTL) related to desirable attributes of cowpea were generated. Cowpea genetic improvement activities aim at the development of drought tolerant, phosphorus use efficient, bacterial blight and virus resistant lines through exploiting available genetic resources as well as deployment of modern breeding tools that will enhance genetic gain when grown by sub‐Saharan Africa farmers.     

Simultaneous improvement in cold tolerance and yield of temperate japonica rice (Oryza sativa L.) by introgression breeding

To combine high yield and improved cold tolerance (CT) in a japonica rice variety, ‘Chaoyou1’ (CY1), 324 BC₂F₅ introgression lines (ILs) selected for CT from 11 CY1 BC₂F₄ populations were evaluated in replicated experiments for their CT at the reproductive and seedling stages. A mean realized heritability of 0.747 was achieved in this study for CT. Evaluation of 116 ILs from five BC populations in replicated experiments under stress and normal conditions identified 18 promising ILs that had greatly improved CT and yield compared with CY1. Detailed comparisons between the ILs and CY1 for CT and yield‐related traits under stress and non‐stress conditions provided useful information and better understanding of important issues such as donor selection, selection efficiency and associated changes in non‐target traits in the BC breeding process. The large numbers of CT ILs developed provide useful materials for genetic, physiological and molecular dissection of CT and yield traits using DNA markers and ‐omic tools, and as parents for further improving these traits by designed QTL pyramiding.     

Pre-emptive breeding to control wheat rusts

Summary Pre-emptive or anticipatory breeding for resistance is breeding for resistance to future pathotypes. It is assumed that these will be derivatives of currently frequent pathotypes that need to mutate with respect to single host resistance genes in order to attack widely-grown cultivars. Success in this approach depends on relevant knowledge of the pathogenicity phenotypes and host resistance genes that occur throughout the wheat-growing areas. Because durability of resistance cannot be assumed, resistance breeding strategies are usually supported with the maintenance of genetic diversity to provide buffering against extreme crop losses in the event of significant pathogenic changes.     

从基因组学到蛋白质组学：棉花分子生物学研究进展

 花基因组计划正在实施,功能基因组学在棉花研究领域扮演着越来越重要的角色。近年来,国内外的研究者在棉花基因组学及蛋白质组学研究领域内取得了比较大的研究进展,本文从棉花遗传图谱、物理图谱的构建,棉花功能基因组、蛋白质组学技术、棉花蛋白质组学研究等方面入手,就棉花分子生物学研究近况进行概述。     

Application of biotechnology in breeding lentil for resistance to biotic and abiotic stress

Summary Lentil is a self-pollinating diploid (2n = 14 chromosomes) annual cool season legume crop that is produced throughout the world and is highly valued as a high protein food. Several abiotic stresses are important to lentil yields world wide and include drought, heat, salt susceptibility and iron deficiency. The biotic stresses are numerous and include: susceptibility to Ascochyta blight, caused by Ascochyta lentis; Anthracnose, caused by Colletotrichum truncatum; Fusarium wilt, caused by Fusarium oxysporum; Sclerotinia white mold, caused by Sclerotinia sclerotiorum; rust, caused by Uromyces fabae; and numerous aphid transmitted viruses. Lentil is also highly susceptible to several species of Orabanche prevalent in the Mediterranean region, for which there does not appear to be much resistance in the germplasm. Plant breeders and geneticists have addressed these stresses by identifying resistant/tolerant germplasm, determining the genetics involved and the genetic map positions of the resistant genes. To this end progress has been made in mapping the lentil genome and several genetic maps are available that eventually will lead to the development of a consensus map for lentil. Marker density has been limited in the published genetic maps and there is a distinct lack of co-dominant markers that would facilitate comparisons of the available genetic maps and efficient identification of markers closely linked to genes of interest. Molecular breeding of lentil for disease resistance genes using marker assisted selection, particularly for resistance to Ascochyta blight and Anthracnose, is underway in Australia and Canada and promising results have been obtained. Comparative genomics and synteny analyses with closely related legumes promises to further advance the knowledge of the lentil genome and provide lentil breeders with additional genes and selectable markers for use in marker assisted selection. Genomic tools such as macro and micro arrays, reverse genetics and genetic transformation are emerging technologies that may eventually be available for use in lentil crop improvement.