Conventional and contemporary approaches for drought tolerance rice breeding: Progress and prospects

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice-growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio-biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought-tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome-wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics-assisted breeding programmes to develop high-yielding drought-tolerant rice cultivars.     

Genomics-assisted breeding in fruit trees

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.     

黄淮麦区Fhb1基因的育种应用

小麦赤霉病是由禾谷镰孢菌引起的一种世界性重要病害,严重威胁小麦生产安全。黄淮麦区作为我国小麦主产区,赤霉病危害日趋严重,因缺乏半冬性抗源,抗赤霉病育种进展缓慢。Fhb1基因是迄今发现的效应最大、抗性最稳定,也是被广泛应用于全球小麦赤霉病抗性育种的主效基因,但Fhb1基因在黄淮麦区尚未被广泛应用。本研究以感病品种矮抗58为轮回亲本, H35为Fhb1基因供体亲本,通过有限回交和分子标记辅助选择,同时利用双单倍体育种和传统系谱选育两种方法,培育出了一批综合性状较好、具有Fhb1基因的优良新品系,其中徐麦DH9和徐麦17252经多年鉴定均达到中抗水平。在以徐麦36和徐麦2023为杂交父本的后代品系中,含Fhb1基因的家系赤霉病平均抗性明显优于感病对照。Fhb1基因的导入显著提高了赤霉病抗性,但部分家系对赤霉病仍旧表现出高感水平,说明赤霉病抗性还受到Fhb1基因以外其他遗传因素的显著影响。本研究为Fhb1基因在黄淮麦区抗赤霉病小麦育种中的应用提供了成功的经验。     

A comparison between single seed descent and early cross selection in wheat breeding

Summary Two selection procedures in wheat breeding were compared on the basis of their ability to supply high yielding inbred lines. The first procedure consists of an early selection between crosses in the F₃ generation, based on cross performance. In the second procedure selection is postponed until the F₆, which is derived by single seed descent. The two procedures are evaluated in a two year test, using pseudo-lines of spring wheat. These pseudo-lines consist of mixtures of varieties and enable an estimation of the true genetic parameters. In this way the accuracy of the predictions can be examined.The first year of this comparison comprised the actual selection process and in the second year an F₆ and F₇ generation were mimicked, based on the selected lines of the F₃ and F₆ respectively, and evaluated in a large yield test. This paper gives the final results after the second year. From the first year it was found that the F₃ cross predictions were very inaccurate, whereas selection in the SSD-F₆ appeared to perform well. This resulted in a higher yielding set of lines evolving from the SSD-F₆. Despite a pronounced genotype-year interaction this difference in yield level was also found between the F₇ and the F₆ lines, derived from the selected crosses in the F₃. We conclude that the early selection procedure is not advantageous compared to the fast SSD procedure.     

A comparison between single seed descent and early cross selection in wheat breeding

Summary Two selection procedures in wheat breeding were compared on the basis of their ability to supply high yielding inbred lines. The first procedure consists of an early selection between crosses in the F₃ generation, based on predictions of the cross mean and the between line variance. In the second procedure selection is postponed until the F₆, which is derived by single seed descent. The two procedures are evaluated in a two year test, using pseudo-lines of spring wheat. These pseudo-lines consist of mixtures of varieties and enable an estimation of the exact genetic parameters. In this way the accuracy of the predictions can be examined.In case of early selection, it appears that the predictions of the cross mean and especially the between line variance are very inaccurate. This is caused by the effects of plot size, intergenotypic competition and, to a lesser extent, dominance and/or epistasis. It results in an erroneous ranking of the crosses and the discarding of the potentially best cross. The F₆-SSD line estimates are much more accurate and thus the better lines are indeed selected. A first comparison between the two selection procedures therefore indicates a preference to the SSD method.     

Molecular markers and their applications in wheat breeding

In recent years, considerable emphasis has been placed on the development of molecular markers to be used for a variety of objectives. This review attempts to give an account of different molecular markers—restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), sequence-tagged sites (STS), DNA amplification fingerprinting (DAF), amplified fragment length polymorphisms (AFLPs) and microsatellites (STMS)—currently available for genome mapping and for tagging different traits in wheat. Other markers, including microsatellite-primed polymerase chain reaction (MP-PCR), expressed sequence tags (ESTs) and single nucleotide polymorphisms (SNPs) are also discussed. Recent information on synteny in cereal genomes, marker-assisted selection, marker validation and their relevance to cereal breeding in general and wheat breeding in particular are also examined.     

Breeding for Fusarium head blight resistance in wheat—Progress and challenges

Fusarium head blight is among the most extensively studied fungal diseases of wheat and other small grain cereals due to its impact on yield and quality, but particularly due to its potential to produce mycotoxins, which are harmful to humans and animals. Since our last comprehensive review on QTL mapping and marker-assisted selection for FHB resistance in wheat in 2009, numerous studies have been conducted to identify, validate or fine-map resistance QTL. The main aim of this review is to update and summarize findings on FHB resistance breeding of wheat published during the last decade. Furthermore, we compiled a user-friendly table listing FHB resistance QTL data providing a valuable resource for further FHB resistance research. The role of morphological and phenological traits on FHB resistance and possible consequences for resistance breeding are discussed. This review concentrates current knowledge on breeding for FHB resistance and suggests strategies to enhance resistance by deploying molecular breeding methods, including marker-assisted and genomic selection.     

Impact of plant genetic resources on wheat breeding

This article describes the impact of plant genetic resources on wheat breeding. It defines the important contribution of N.I. Vavilov Institute (St. Petersburg, Russia) to broadening the genetic diversity of new wheat cultivars. Special attention is given to conducting a comprehensive evaluation of intraspecific variability for valuable characters, including: 1) formation of special subcollections, consisting of accessions with useful characters and accessions representing intraspecies diversity for a given character; 2) revealing genetic differences among phenotypically superior accessions; 3) determining a genetic system of intraspecific variability for a given character; 4) formation of a genetic collection; 5) revealing and developing the donors of useful characters. An example using plant height shows that the proposed research approach adequately determines the genetic potential of species and reveals the most effective genes for practical uses. It is assumed that the main sources of genes for breeding Triticum aestivum L. in order of importance will remain: 1) intraspecific diversity of T. aestivum itself; 2) other Triticum species; 3) other genera of the Triticeae Dum. tribe (particularly Aegilops L.); 4) more remote genera of the Poaceae Barnh. botanical family. It is stressed that existing diversity of T. aestivum has been poorly investigated genetically and only partially used by breeders. Properly evaluated, it can provide multiple solutions for traditional and new problems of wheat improvement. This revised version was published online in August 2006 with corrections to the Cover Date.     

The relations of broad nematode resistance to quality characteristics as a consequence of marker-assisted selection in potato breeding programs

Cultivating resistant varieties of potato is the most effective and environmentally sound method of protecting potato crops against pests and diseases. Potato cyst nematodes (PCN) are major nematode pests causing severe constraints in potato production worldwide. There are five pathotypes of Globodrea rostochiensis (Ro1–Ro5) and three of G. pallida Pa1–Pa3. Cultivation of potato varieties with broad nematode resistance may influence the growth of the wide spectrum of PCN pathotypes, but there is limited availability of such varieties on the market. The use of molecular markers allows for the effective selection of resistant genotypes at early stages of breeding. However, the impact of early selection for nematode resistance on the agronomic value of the final selected clones is a cause of concern for potato breeders. This study investigates the relationships between the presence of the combined resistance genes H1, Gro1-4 and GpaV_vrn, which confer resistance to the nematodes, and certain agricultural traits. Clones with broad nematode resistance conferred by the genes H1, Gro1-4 and GpaV_vrn presented yields and tuber morphology traits similar to those of the clones without identified resistance genes.     

The alternative breeding approaches for improving yield gains and stress response in pigeonpea (Cajanus cajan)

Pigeonpea is an important food legume crop of semi‐arid tropical regions. Plateauing of pigeonpea yield has been worrying breeders for the past 6–7 decades. Serious breeding efforts made during this period resulted in various high‐yielding and disease resistant cultivars. However, the gains in pigeonpea productivity have been modest. The authors, while reviewing this situation, conclude that long generation turnover, complexity of biological traits, low selection response and overreliance upon pedigree breeding present the key bottlenecks for this situation. In this paper, some alternative breeding approaches and technologies are suggested for the genetic enhancement of yield stability and stress response of pigeonpea.     

DNA and morphological markers for a Russian wheat aphid resistance gene

The Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), is a significant insect pest of wheat worldwide. Morphological and molecular markers associated with RWA resistance could be used to increase the accuracy and efficiency of selection of resistant germplasm and facilitate transfer to desirable wheat genotypes. The objective of this work was to identify microsatellite (SSR) markers linked to the RWA resistance gene (Dn4) and glume-colour gene (Rg2) using a population of F₂-derived F₃ families originating from a cross between a susceptible line (synthetic hexaploid-11) and a resistance cultivar (Halt). Two microsatellite markers Xgwm106 and Xgwm337 flanked Dn4 on the short arm of chromosome 1D at 5.9 and 9.2 cM, respectively. Two other microsatellite markers, Xpsp2999 and Xpsp3000, at the distal part of this chromosome arm are linked to Dn4 and to Rg2. The accuracy and efficiency of marker-assisted selection were calculated for homozygous Dn4Dn4 genotypes in the F₂ generation. The gene Rg2 for red glume colour can also be used for marker-assisted selection of Dn4 gene individually and in combination with microsatellite markers. When used together, the closest markers Xgwm106 and Xgwm337, provide 100% accuracy and 75% efficiency. One hundred percent accuracy is also achieved when the morphological marker red glume is used in combination with either Xgwm106 or Xgwm337. Using these flanking markers, it may be possible to fix resistance to RWA in the first segregating generation of an F₂ population without infestation with aphids.     

Normalization method for canopy temperature as an indirect indicator of yield potential in wheat breeding programs

Canopy temperature (CT) is often related to potential yield and is a possible yield indicator in breeding programs. However, it is difficult to evaluate genetic variations of CT accurately in large-scale investigations, such as breeding programs, because CT is strongly affected by environmental conditions. In this study, to precisely evaluate these genetic variations, we determined the environmental factors that affect CT measurement and proposed a convenient normalization method to minimize their influence. We measured the CT of CT-high or CT-low cultivars in the field under various conditions. We found that as the sun and shade levels were alternated, the CT changed within seconds; the position in the field also critically affected the CT. However, even under these conditions, the differences between cultivars became clearer if CT was normalized by neighboring lines. Additionally, we revealed that CT measurements between 12:00 and 15:00 maximized the difference between cultivars. Using our normalization technique under the favorable conditions specified can help breeders select high-yield lines using CT in breeding programs.     

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.     

Genomic resources for breeding crops with enhanced abiotic stress tolerance

To meet the challenges of climate change, exploring natural diversity in the existing plant genetic resource pool as well as creation of new mutants through chemical mutagenesis and molecular biology is needed for developing climate‐resilient elite genotypes. Ever‐increasing area under existing abiotic stresses as well as emerging abiotic stress factors and their combinations have further added to the problems of the current crop improvement programmes. However, with the advancement in modern techniques such as next‐generation sequencing technologies, it is now possible to generate on a whole‐genome scale, genomic resources for crop species at a much faster pace with considerably less efforts and money. The genomic resources thus generated will be useful for various plant breeding applications such as marker‐assisted breeding for gene introgression, mapping QTLs or identifying new or rare alleles associated with a particular trait. In this article, we discuss various aspects of generation of genomic resources and their utilization for developing abiotic stress‐tolerant crops to ensure sustainable agricultural production and food security in the backdrop of rapid climate change.     

Directions in breeding for winter wheat yield and quality in South Africa from 1930 to 1990

Summary Changes in the genetic yield and quality potential of South African winter wheat cultivars since 1930 were investigated by means of canonical variate analysis. Yield potential improved by 87%, while test weight and protein percentage changed marginally. Flour colour improved mostly since 1965, but advancement of flour yield declined after 1984. Dough strength increased since 1930, yet current levels of dough strength should not be exceeded. When compared to farinograph assessment of dough strength, mixograph dough development time appears to be a less sensitive indicator of variation in dough strength. Selection on the basis of mixograph dough development time only, could influence a breeder's perception of the dough quality profile of his breeding programme. Protein efficiency was maintained despite improvement in yield potential. Baking quality improved by 20%. The genetic winter wheat potential advanced significantly since 1930 in meeting the increased nutritional demands of the South African population.Abbreviations BSI Baking strength index - CBP Chorleywood Breadmaking Process - CVA Canonical variate analysis - CV₁ First canonical variate - CV₂ Second canonical variate - FCL Flour colour - FDT Farinograph dough development time - FLY Flour yield - FPC Flour protein content - FST Farinograph stability - FWS Farinograph water absorption - GPR Grain protein content - GPY Grain protein yield - LFV Loaf volume - MDT Mixograph dough development time - SDS SDS sedimentation volume - STY Starch yield - TSW Test weight - WBS Water absorption - YLD Yield     

Selection for yield in wheat breeding

Summary If selection based on F₃ yield tests is to be effective, the yield tests must be successful in discriminating among yield genotypes. The available literature indicates that simple tests with limited or no replication are not very effective, although more extensive, replicated tests may be.Data from an experiment comparing F₃ yield tests with a single seed descent procedure showed that F₃ selection based on a two-replicate test with single seed descent procedure did not justify the extra work involved.     

QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review

During the past decade, numerous studies have been published on molecular mapping of Fusarium head blight (FHB) resistance in wheat. We summarize the relevant findings from 52 quantitative trait loci (QTL) mapping studies, nine research articles on marker-assisted selection and seven on marker-assisted germplasm evaluation. QTL for FHB resistance were found on all wheat chromosomes except chromosome 7D. Some QTL were found in several independent mapping studies indicating that such QTL are stable and therefore useful in breeding programmes. We summarize and update current knowledge on the genetics of FHB resistance in wheat resulting from QTL mapping investigations and review and suggest FHB breeding strategies based on the available information and DNA markers.     

Mapping of QTL for resistance against Fusarium head blight in the winter wheat population Pelikan//Bussard/Ning8026

We report on the identification of FHB ( Fusarium head blight) resistance quantitative trait loci (QTL) of the donor 'G93010' (Bussard/Ning8026) in the background of elite breeding material adapted to the central European climate. With a multiple interval mapping method, two major resistance QTL were identified. Qfhs.lfl-7BS/5BL and Qfhs.lfl-6BS reduced FHB severity individually by 30% and 24%. The combination of both QTL decreased disease severity most effectively by about one half. Qfhs.lfl-6BS is most likely identical to Fhb2 , thus, the effectiveness of Fhb2 in central European breeding material has been validated. Qfhs.lfl-7BS/5BL overlapped with QTL for plant height and heading date. Nevertheless, the selection of lines combining a good FHB resistance level with an acceptable plant height was possible. As the donors of the QTL have probably not yet been utilized in European breeding material, we identified well-adapted lines of the mapping population as valuable donors for marker-assisted breeding programmes.