New Technologies, Tools and Approaches for Improving Crop Breeding


Most crops were first domesticated about 13 000 to 11 000 years ago. Humans are dependent on crops for survival, and from the beginnings of agriculture have been energetically involved in developing crops that better serve their needs (Allard 1999). During the last decades breeding has contributed approximately a 50% contribution to increasing the world's food crop production. However, plant breeding only began to adopt a scientific approach in the 1900s, when Mendel's hybridization experiment was rediscovered. Mendelian genetics and the development of the statistical concepts of randomization and replication had considerable impact on plant breeding methods (Hallauer et al. 1988). In spite of the fact that scientific crop breeding has only existed for one century, it is a discipline that is developing very quickly. The major objective of crop breeding programs is to develop new genotypes that are genetically superior to those currently available for specific environments. To achieve this objective, breeders employ a range of selection methods and technologies (Hallauer et al. 1988; Falconer and Mackay 1996; Allard 1999).

As the world's population continues to grow rapidly and becomes more demanding, the pressure on resources is increasing, whilst climate change poses further challenges. The balance between the supply and demand of the major food crops is fragile, fueling concerns for long-term global food security. The need to accelerate plant breeding for increased yield potential and better adaptation to drought and other abiotic stresses is an issue of increasing urgency. The global population is facing a common challenge of providing safe, nutritious and affordable food, given the constraints of land, water, and energy and in the face of climate change. The sustainable exploitation of biological resources for a secure and healthy food supply, animal feed and a wide range of sustainable materials and technical products will require careful husbandry of land and a shift to systems that produce more from less in a sustainable manner. With this common goal, OPTICHINA (Breeding to Optimize Chinese Agriculture), an EU-China partnership initiative in crop breeding was launched in June of 2011. The first project workshop was held shortly after the launch, and focused on new technologies and methods in crop molecular breeding. This special issue of Journal of Integrative Plant Biology publishes key presentations and topics addressed in this workshop.

New Technologies for the New Era of Crop Breeding

Molecular genetics and associated technologies have greatly contributed to our understanding of the inheritance of targeted traits in plant breeding, which in turn open new ways of improving the efficiency of breeding programs. High-throughput sequencing is a revolutionary technological innovation in DNA sequencing. This technology has the advantageous characteristics of extremely low cost single-base sequencing and overwhelmingly high data output.

Gao et al. (2012) Recent progress using high-throughput sequencing technologies in plant molecular breeding

Gao et al. (2012) present a thorough review on the application of high throughput (or next generation) sequencing technology to genomic and functional genomic molecular breeding studies. This technology has brought novel research methods and solutions to the research fields of genomics and post-genomics, and is leading a revolution in the field of molecular breeding. The new high-throughput sequencing technology driving this revolution generates massive amounts of sequence data faster and more cheaply than the traditional method. Consequently, it is expected that whole-genome molecular breeding will develop new super crop varieties that contain multiple desirable traits.

Zhou et al. (2012)ZmcrtRB3 encodes a carotenoid hydroxylase that affects the accumulation of α-carotene in maize kernel

In maize, α-carotene is one of the important components of pro-vitamin A, which can be converted into vitamin A in the human body. Zhou et al. (2012) mapped ZmcrtRB3 in a QTL cluster for carotenoid-related-traits on chromosome 2 (bin 2.03) in a recombinant inbred line (RIL) population derived from By804 and B73. Candidate gene-association analysis identified 18 polymorphic sites in ZmcrtRB3 significantly associated with one or more carotenoid-related traits in 126 diverse yellow maize RILs. Their results indicate that the enzyme encoded by ZmcrtRB3 plays a role in hydrolyzing α-carotene and β-carotene, while polymorphisms in ZmcrtRB3 contributed to more variation in α-carotene content than that of β-carotene. SNP1343 in 5’UTR and SNP2172 in the second intron had consistent effects on α-carotene content and composition, and therefore can be used to develop functional markers for applying marker-assisted selection in the improvement of pro-vitamin A carotenoids in maize kernels.

Yu et al. (2012) Metabolic engineering of plant-derived (E)-β-farnesene synthase genes for a novel type of aphid-resistant genetically-modified crop plants

Transgenic crops engineered for resistance to aphids via a non-toxic mode of action could be an efficient strategy in pest control. (E)-β-Farnesene (EβF) synthases catalyze the formation of EβF, a main component of the alarm pheromone in the chemical communication within these species. Engineering of crop plants capable of synthesizing and emitting EβF could cause repulsion of aphids and also the attraction of natural enemies, thus minimizing aphid infestation. Xia et al. (2012) reviewed the effects of aphids on host plants, plant defenses against aphid herbivory and the recruitment of natural enemies for aphid control. The plant-derived EβF synthase genes cloned to date along with their potential roles in generating novel aphid resistance via GM approaches are also discussed.

Cabrera-Bosquet et al. (2012) High-throughput phenotyping and genomic selection: The frontiers of crop breeding converge

Genomic selection and high-throughput phenotyping have recently captivated the interest of the crop breeding community from both public and private sectors world-wide. Main aspects of both approaches together with some case studies are presented in the review by Cabrera-Bosquet et al. (2012). The authors believe that both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Genomic selection and high-throughput phenotyping have in common their empirical approaches, allowing breeders to use genome profile or phenotype without understanding the underlying biology. These empirical approaches rely in the capacity for extensive data collection and analysis, together with advances in robotics.

New Tools for the New Era of Crop Breeding

Most of the important characteristics that plant breeders wish to improve vary continuously, i.e. they are quantitative traits, among which are yield and yield components, end-use qualities, adaptation, and various biotic and abiotic resistances or tolerances. Understanding the genetics of these traits allows the application of genotypic selection in the breeding process, and is of fundamental significance as plant breeding shifts from the ‘selection of best line’ to a much more ‘design-led’ approach including the identification and selection of best combinations of useful genomic regions. A thorough understanding of genes that underlie agronomically important traits in crops would greatly increase agricultural productivity. However, new tools are essential in identifying the genes of breeding traits.

Zhang et al. (2012) The statistical power of inclusive composite interval mapping in detecting digenic epistasis showing common F2 segregation ratios

Epistasis is a commonly observed genetic phenomenon and an important source of variation of complex traits, which could maintain additive variance and therefore assure the long-term genetic gain in breeding. Inclusive composite interval mapping (ICIM) is able to identify epistatic QTLs no matter whether the two interacting QTLs have any additive effects. Zhang et al. (2012) conducted a simulation study to evaluate detection power and false discovery rate (FDR) of ICIM epistatic mapping by considering F2 and DH populations, different F2 segregation ratios (representing commonly observed epistasis) and population sizes. Their simulation results indicated that estimations of QTL locations and effects were unbiased, and the detection power of epistatic mapping was largely affected by population size, heritability of epistasis, and the amount and distribution of genetic effects. When the same LOD threshold was used, detection power of QTL was higher in the F2 population than that in the DH population; meanwhile FDR in F2 was also higher than that in DH. However, when compared with additive QTL mapping, much larger populations are needed in order to increase the mapping precision and reduce false positives.

Yang et al. (2012) A sequential quantitative trait locus fine-mapping strategy using recombinant-derived progeny

Although advances have been made in QTL cloning, the majority of QTLs remain unknown because of their low heritability and minor contributions to phenotypic performance. Yang et al. (2012) summarized key advantages and disadvantages of current QTL fine-mapping methodologies, and then introduced a sequential QTL fine-mapping strategy based on both genotypes and phenotypes of progeny derived from recombinants. With this mapping strategy, experimental errors could be dramatically diminished so as to reveal the authentic genetic effect of target QTLs. This mapping strategy has proved to be very powerful in narrowing down QTL regions, particularly minor-effect QTLs, as revealed by fine-mapping of various resistance QTLs in maize.

Zhao et al. (2012) Identification and fine mapping of rhm1 locus for resistance to Southern corn leaf blight in maize

For Southern corn leaf blight (SCLB), rhm1 is a major recessive disease resistance gene. To further narrow down its genetic position, Zhao et al. (2012) developed F2 and BC1F1 populations from the cross between resistant (H95rhm) and susceptible (H95) parents. Using newly developed markers, rhm1 was mapped to a 8.56 kb interval between InDel marker IDP961-503 and SSR marker A194149-1. Three polymorphic markers IDP961-504, IDP B2-3 and A194149-2 were shown to be co-segregated with rhm1 gene, which can be directly used for molecular breeding of resistance to Southern corn leaf blight in maize.

Love et al. (2012) InterStoreDB: A generic integration resource for genetic and genomic data

Associating phenotypic traits and QTL with causative regions of the underlying genome is a key goal in agricultural research. Love et al. (2011) present a generic integration resource called InterStoreDB to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. Genetic maps are visualised and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.

New Approaches for the New Era of Crop Breeding

Molecular marker techniques are influencing the breeding process from parental selection and cross prediction, to introgression of known genes and population enhancement. The new approaches will sustain the world's food productivity.

Ali and Yan (2012) Disease resistance in maize and the role of molecular breeding in defending against global threat

Diseases are a potential threat to global food security but plants have evolved an extensive array of methodologies to cope with the invading pathogens. Ali and Yan (2012) reviewed the basic terminologies in disease resistance in crop plants, with a focus on resistance in maize. This review describes the whole mechanism of disease resistance and focuses on future research perspectives along with the role of genetic diversity, association mapping, combined linkage and association mapping and genomic selection in overcoming this devastating global problem.

Please note this paper (Ali and Yan 2012) was published early in the regular March issue.

Masuka et al. (2012) Phenotyping for abiotic stress tolerance in maize

Germplasm combining tolerance to several complex polygenic-inherited abiotic and biotic stresses will be critical to the resilience of cropping systems in the face of climate change. Masuka et al. (2012) described key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen. Yield is a function of many processes throughout the plant cycle thus integrative traits that encompass crop performance over time or organization level (i.e. canopy level) will provide a better alternative to instantaneous measurements which only provide a snapshot of a given plant process. New phenotyping tools based on remote sensing are introduced, including non-destructive measurements of growth-related parameters based on spectral reflectance and infrared thermometry to estimate plant water status.

Cao et al. (2012) Identification and validation of a major quantitative trait locus for slow-rusting resistance to stripe rust in wheat

Stripe (yellow) rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks (Pst), is one of the most important wheat diseases and causes significant yield losses. Cao et al. (2012) used a recombinant inbred (RI) population to study the resistance to wheat stripe rust strain CYR32 at both the seedling and adult-plant stages. Four resistance QTLs were detected in this population, in which the major one, designated as Yrq1, was mapped on chromosome 2DS. Of the 19 polymorphic simple sequence repeats (SSRs) in the RI population, 17 SSRs were mapped in the homeologous group 2 chromosomes near Yrq1 region and 8 SSRs were genetically mapped in the 2.7-cM region of Yrq1, providing abundant DNA markers for fine-mapping of Yrq1 and marker-assisted selection in the wheat breeding program. The effectiveness of Yrq1 was validated in an independent population, indicating this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

Bai et al. (2012) Yield-related QTLs and their applications in rice genetic improvement

Different mapping populations have been used to explore QTLs controlling yield-related traits. Bai et al. (2012) reviewed yield-related QTLs and their applications in rice genetic improvement. Primary populations such as F2 and recombinant inbred line populations have been widely used to discover QTLs in rice genome-wide, with hundreds of yield-related QTLs detected. Use of advanced populations such as near isogenic lines (NILs) is efficient for further fine-mapping and cloning target QTLs. NILs for primarily identified QTLs have been proposed and confirmed to be the ideal population for map-based cloning. To date, 20 QTLs directly affecting rice grain yield and its components have been cloned with NIL-F2 populations, and 14 new grain yield QTLs have been validated in the NILs. The molecular mechanisms of a continuously increasing number of genes are being unveiled, which aids in the understanding of the formation of grain yield. Favorable alleles for rice breeding have been identified in natural cultivars and wild rice by association analysis of known functional genes with target trait performance. Optimum combination of favorable alleles has the potential to increase grain yield via use of functional marker-assisted selection.

Parry and Hawkesford (2012) An integrated approach to crop genetic improvement

There is a predicted need to increase crop production by at least 70% by 2050 and therefore an urgent need to develop novel and integrated approaches that will both increase production per unit area and simulataneously improve the resource use efficiency of crops. In order to better understand the relationship between genotype, component traits, and environment over time, a multidisciplinary approach must be adopted to both understand the underlying processes and identify candidate genes, QTLs and traits that can be used to develop improved crops. Parry and Hawkesford (2012) present an integrated approach to crop genetic improvement. They believe that molecular plant breeding has the potential to deliver substantial improvements, once the component traits and the genes underlying these traits have been identified. Identified traits will be incorporated into new cultivars using conventional or biotechnological tools.

Martin A. J. Parry 1 Jiankang Wang 2 José Luis Araus 3 1 Special Issue Editor, Rothamsted Research, Harpenden, Herts, UK 2 Special Issue Editor, Chinese Academy of Agricultural Sciences, Beijing, China 3 Special Issue Editor, University of Barcelona, Barcelona, Spain

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