Special Issue: Methods in Crop Molecular Breeding(1)   

April 2012, Volume 54 Issue 4, Pages 210C279.

Cover Caption: Methods in Crop Molecular Breeding
About the cover: Thermal imagery is among the most promising techniques to assess genotypic variability in crop water status, a factor in yield performance in response to stresses such as water deficit or heat. The paper of Masuka et al. (pp 238C249) reports on novel technologies to evaluate phenotypic performance under different stress conditions together with the use of different phenotyping techniques to handle the problems associated with spatial variability exhibited by field trials.


New Technologies, Tools and Approaches for Improving Crop Breeding  
Author: Martin A. J. Parry, Jiankang Wang and Jose Luis Araus
Journal of Integrative Plant Biology 2012 54(4): 210-214
Published Online: March 12, 2012
DOI: 10.1111/j.1744-7909.2012.01114.x

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. Themajor 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 sustainablematerials 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.

Abstract (Browse 2070)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Invited Expert Reviews
Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular Breeding  
Author: Qiang Gao, Guidong Yue, Wenqi Li, Junyi Wang, Jiaohui Xu and Ye Yin
Journal of Integrative Plant Biology 2012 54(4): 215-227
Published Online: March 12, 2012
DOI: 10.1111/j.1744-7909.2012.01115.x

High-throughput sequencing is a revolutionary technological innovation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi-faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.

Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y (2012) Recent progress using high-throughput sequencing technologies in plant molecular breeding. J. Integr. Plant Biol. 54(4), 215–227.

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A Sequential Quantitative Trait Locus Fine-Mapping Strategy Using Recombinant-Derived Progeny  
Author: Qin Yang, Dongfeng Zhang and Mingliang Xu
Journal of Integrative Plant Biology 2012 54(4): 228-237
Published Online: February 20, 2012
DOI: 10.1111/j.1744-7909.2012.01108.x

A thorough understanding of the quantitative trait loci (QTLs) that underlie agronomically important traits in crops would greatly increase agricultural productivity. 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. Here we summarize the key advantages and disadvantages of current QTL fine-mapping methodologies, and then introduce 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. The number of progeny required to detect QTLs at various R2 values was calculated, and the backcross generation suitable to start QTL fine-mapping was also estimated. 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. Application of this sequential QTL mapping strategy should accelerate cloning of agronomically important QTLs, which is currently a substantial challenge in crops.

Yang Q, Zhang D, Xu M (2012) A sequential QTL fine-mapping strategy using recombinant-derived progeny. J. Integr. Plant Biol. 54(4), 228–237.

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Phenotyping for Abiotic Stress Tolerance in Maize  
Author: Benhilda Masuka, Jose Luis Araus, Biswanth Das, Kai Sonder and Jill E. Cairns
Journal of Integrative Plant Biology 2012 54(4): 238-249
Published Online: March 23, 2012
DOI: 10.1111/j.1744-7909.2012.01118.x

The ability to quickly develop germplasm having tolerance to several complex polygenic inherited abiotic and biotic stresses combined is critical to the resilience of cropping systems in the face of climate change. Molecular breeding offers the tools to accelerate cereal breeding; however, suitable phenotyping protocols are essential to ensure that the much-anticipated benefits of molecular breeding can be realized. To facilitate the full potential of molecular tools, greater emphasis needs to be given to reducing the within-experimental site variability, application of stress and characterization of the environment and appropriate phenotyping tools. Yield is a function of many processes throughout the plant cycle, and 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 provide only a snapshot of a given plant process. Many new phenotyping tools based on remote sensing are now available including non-destructive measurements of growth-related parameters based on spectral reflectance and infrared thermometry to estimate plant water status. Here we describe key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen.

Masuka B, Araus JL, Das B, Sonder K, Cairns JE (2012) Phenotyping for abiotic stress tolerance in maize. J. Integr. Plant Biol. 54(4), 238–249.

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An Integrated Approach to Crop Genetic Improvement  
Author: Martin A. J. Parry and Malcolm J. Hawkesford
Journal of Integrative Plant Biology 2012 54(4): 250-259
Published Online: February 20, 2012
DOI: 10.1111/j.1744-7909.2012.01109.x

The balance between the supply and demand of the major food crops is fragile, fueling concerns for long-term global food security. The rising population, increasing wealth and a proliferation of non-food uses (e.g. bioenergy) has led to growing demands on agriculture, while increased production is limited by greater urbanization, and the degradation of land. Furthermore, global climate change with increasing temperatures and lower, more erratic rainfall is projected to decrease agricultural yields. There is a predicted need to increase food production by at least 70% by 2050 and therefore an urgent need to develop novel and integrated approaches, incorporating high-throughput phenotyping that will both increase production per unit area and simultaneously improve the resource use efficiency of crops. Yield potential, yield stability, nutrient and water use are all complex multigenic traits and while there is genetic variability, their complexity makes such traits difficult to breed for directly. Nevertheless molecular plant breeding has the potential to deliver substantial improvements, once the component traits and the genes underlying these traits have been identified. In addition, interactions between the individual traits must also be taken into account, a demand that is difficult to fulfill with traditional screening approaches. Identified traits will be incorporated into new cultivars using conventional or biotechnological tools. 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 MAJ, Hawkesford MJ (2012) An integrated approach to crop genetic improvement. J. Integr. Plant Biol. 54(4), 250–259.

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          Research Articles
ZmcrtRB3 Encodes a Carotenoid Hydroxylase that Affects the Accumulation of -carotene in Maize Kernel  
Author: Yi Zhou, Yingjia Han, Zhigang Li, Yang Fu, Zhiyuan Fu, Shutu Xu, Jiansheng Li, Jianbing Yan and Xiaohong Yang
Journal of Integrative Plant Biology 2012 54(4): 260-269
Published Online: February 20, 2012
DOI: 10.1111/j.1744-7909.2012.01106.x

α-carotene is one of the important components of pro-vitamin A, which is able to be converted into vitamin A in the human body. One maize (Zea mays L.) ortholog of carotenoid hydroxylases in Arabidopsis thaliana, ZmcrtRB3, was cloned and its role in carotenoid hydrolyzations was addressed. ZmcrtRB3 was mapped in a quantitative trait locus (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 inbred lines. These results indicate that the enzyme ZmcrtRB3 plays a role in hydrolyzing both α- and β-carotenes, while polymorphisms in ZmcrtRB3 contributed more variation in α-carotene than that in β-carotene. Two single nucleotide polymorphisms (SNPs), SNP1343 in 5′untranslated region and SNP2172 in the second intron, consistently had effects on α-carotene content and composition with explained phenotypic variations ranging from 8.7% to 34.8%. There was 1.7- to 3.7-fold change between the inferior and superior haplotype for α-carotene content and composition. Thus, SNP1343 and SNP2172 are potential polymorphic sites to develop functional markers for applying marker-assisted selection in the improvement of pro-vitamin A carotenoids in maize kernels.

Zhou Y, Han Y, Li Z, Fu Y, Fu Z, Xu S, Li J, Yan J, Yang X (2012) ZmcrtRB3 encodes a carotenoid hydroxylase that affects the accumulation of α-carotene in maize Kernel. J. Integr. Plant Biol. 54(4), 260–269.

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The Statistical Power of Inclusive Composite Interval Mapping in Detecting Digenic Epistasis Showing Common F2 Segregation Ratios  
Author: Luyan Zhang, Huihui Li and Jiankang Wang
Journal of Integrative Plant Biology 2012 54(4): 270-279
Published Online: February 21, 2012
DOI: 10.1111/j.1744-7909.2012.01110.x

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 quantitative trait loci (QTLs) no matter whether the two interacting QTLs have any additive effects. In this article, we conducted a simulation study to evaluate detection power and false discovery rate (FDR) of ICIM epistatic mapping, by considering F2 and doubled haploid (DH) populations, different F2 segregation ratios and population sizes. 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 likelihood of odd (LOD) threshold was used, detection power of QTL was higher in F2 population than power in DH population; meanwhile FDR in F2 was also higher than that in DH. The increase of marker density from 10 cM to 5 cM led to similar detection power but higher FDR. In simulated populations, ICIM achieved better mapping results than multiple interval mapping (MIM) in estimation of QTL positions and effect. At the end, we gave epistatic mapping results of ICIM in one actual population in rice (Oryza sativa L.).

Zhang L, Li H, Wang J (2012) The statistical power of inclusive composite interval mapping in detecting digenic epistasis showing common F2 segregation ratios. J. Integr. Plant Biol. 54(4), 270–279.

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