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Crop Science : Just Published


Accepted, edited articles are published here after author proofing to provide rapid publication and better access to the newest research. Articles are compiled into issues at dl.sciencesocieties.org/publications/cs, which includes the complete archive.

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Lorenz, A.J., T.J. Gustafson, J.G. Coors, and N. de Leon. 2009. Breeding Maize for a Bioeconomy: A Literature Survey Examining Harvest Index and Stover Yield and Their Relationship to Grain Yield. Crop Sci. doi: 10.2135/cropsci2009.02.0086

Current issue: Crop Sci. 56(3)


    • Baohua Wang, Xavier Draye, Zhengsheng Zhang, Zhimin Zhuang, O. Lloyd May, Andrew H. Paterson and Peng W. Chee
      Advanced Backcross Quantitative Trait Locus Analysis of Fiber Elongation in a Cross between Gossypium hirsutum and G. mustelinum

      In an effort to explore the secondary gene pool for the enhancement of upland cotton (Gossypium hirsutum L.) germplasm, we developed advanced-generation backcross populations by crossing G. hirsutum (PD94042) and Gossypium mustelinum Miers ex Watt (AD4–8), then backcrossing to the G. hirsutum parent for three cycles. Genome-wide mapping revealed introgressed alleles at an average of 13.8% of loci in each BC3F1 plant, collectively representing G. (continued)

      Published: April 29, 2016

    • Yadi Xing, Dan Du, Yanhua Xiao, Tianquan Zhang, Xinlong Chen, Ping Feng, XianChun Sang, Nan Wang and Guanghua He
      Fine Mapping of a New Lesion Mimic and Early Senescence 2 ( lmes2 ) Mutant in Rice

      A novel lesion mimic and early senescence 2 (lmes2) mutant was identified from Jinhui10, an indica restorer line in rice (Oryza sativa L.), which was treated with ethyl methane sulfonate (EMS). Lmes2 began to develop disease-like lesions on leaves at the seedling stage and aged leaves that had the maximum distribution of such lesions began to senesce. Compared with the wild-type, a low content of chlorophylls was observed, while the proline content increased in proportion to the development of lesion mimics. In addition, the photosynthetic rate and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities fell very significantly, which indicates that lmes2 develops early senescence. (continued)

      Published: April 29, 2016

    • Sivakumar Sukumaran, Xin Li, Xianran Li, Chengsong Zhu, Guihua Bai, Ramasamy Perumal, Mitchell R. Tuinstra, P.V. Vara Prasad, Sharon E. Mitchell, Tesfaye T. Tesso and Jianming Yu
      QTL Mapping for Grain Yield, Flowering Time, and Stay-Green Traits in Sorghum with Genotyping-by-Sequencing Markers

      Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a stay-green high yield inbred) and evaluated in eight environments (location and year combination) in a hybrid background of Tx3042 (a non-stay-green A-line). Phenotyping was conducted for agronomic traits (grain yield and flowering time), physiological traits of stay-green (chlorophyll content [SPAD] and chlorophyll fluorescence [Fv/Fm] measured on the leaves), and green leaf area visual score (GLAVS). This population was genotyped with genotyping-by-sequencing (GBS) technology. (continued)

      Published: April 29, 2016

    • B.T. Campbell, J. Greene, J. Wu and D.C. Jones
      Genetic Variation for Agronomic and Fiber Quality Traits in a Population Derived from High-Quality Cotton Germplasm

      Genetic improvement of fiber quality is necessary to meet the requirements of processors and users of upland cotton (Gossypium hirsutum L.) fiber. To foster genetic improvement of cotton fiber quality, adequate genetic variation for the quantitatively inherited physical properties of cotton is required. Additionally, knowledge of the genetic architecture of fiber quality is needed to design effective breeding strategies to further improve fiber quality. In this study, our objective was to estimate genetic variance components and predict genetic effects for agronomic and fiber quality traits in a population derived from four known genotypic sources of high fiber quality. (continued)

      Published: April 15, 2016

    • Duli Zhao, Vanessa S. Gordon, Jack C. Comstock, Neil C. Glynn and Richard M. Johnson
      Assessment of Sugarcane Yield Potential across Large Numbers of Genotypes using Canopy Reflectance Measurements

      Canopy reflectance indices have been used to monitor plant growth and estimate yields in many field crops. Little is known if canopy reflectance of sugarcane (a complex hybrid of Saccharum spp.) can be used to estimate growth and yield potential across large numbers of genotypes (clones) in the early stages of a breeding program. The objectives of this study were to identify clonal variation in sugarcane canopy reflectance and yield components and to determine if there were any putative relationships between canopy reflectance or reflectance indices and yield variables. In Stage II of the Canal Point sugarcane breeding and cultivar development program (CP program), canopy reflectance data were collected five to six times from each of 156 to 164 randomly selected clones during the growing seasons in 2011 through 2013 using a multispectral radiometer. (continued)

      Published: April 15, 2016

    • Yaqi Wang, Wei Chen, Ye Zhang, Meifeng Liu, Jiejie Kong, Zheping Yu, Ali M. Jaffer, Junyi Gai and Tuanjie Zhao
      Identification of Two Duplicated Loci Controlling a Disease-like Rugose Leaf Phenotype in Soybean

      The disease-like leaf mutant exhibits sensitive symptoms in the absence of pathogens and is an important experimental material for studying leaf development and pathogen resistance mechanisms in plants. We used 60Co γ ray irradiation treatment of a Japanese soybean [Glycine max (L.) Merr.] plant introduction Tamahomore to obtain a new disease-like mutant, designated NT301. The mutant leaves were significantly smaller and thicker than those of the wild-type plant, with a reduction in leaf vein growth and increased growth of leaf mesophyll tissue. The surface of these rugose leaves resembled the symptoms of virus infection. (continued)

      Published: April 15, 2016

    • Vijaya Singh, Chuc T. Nguyen, Zongjian Yang, Scott C. Chapman, Erik J. van Oosterom and Graeme L. Hammer
      Genotypic Differences in Effects of Short Episodes of High-Temperature Stress during Reproductive Development in Sorghum

      Recent studies on sorghum [Sorghum bicolor (L) Moench] showed that episodes of high-temperature stress around anthesis could adversely affect grain yield via effects on pollen germination with varying responses among genotypes. The objectives of this study were to determine the reproductive development phase most sensitive to heat stress and to determine whether genotypic differences in high-temperature tolerance were associated with differences in either cardinal temperatures for pollen germination, the duration of the period of sensitivity to high temperatures, or the extent of the response to high temperature per se. To determine cardinal temperatures, pollen from six genotypes, differing in high-temperature tolerance, was incubated on a gradient plate at temperatures between 10 and 40°C. To identify the critical period of high temperature sensitivity, plants of two genotypes with contrasting high-temperature tolerance were grown under optimum (31 vs. (continued)

      Published: April 15, 2016

    • Alina Liersch, Jan Bocianowski, Henryk Woś, Laurencja Szała, Katarzyna Sosnowska, Teresa Cegielska-Taras, Kamila Nowosad and Iwona Bartkowiak-Broda
      Assessment of Genetic Relationships in Breeding Lines and Cultivars of Brassica napus and Their Implications for Breeding Winter Oilseed Rape

      The level of genetic diversity or similarity between parents has been proposed as a predictor of F1 generation performance and heterosis for seed yield. The objective of this study was to determine the feasibility of using amplified fragment length polymorphism (AFLP) fluorescent-labeled primers to evaluate the genetic relationships between 101 oilseed rape (Brassica napus L.) genotypes to maximize the selection of different parents in a breeding program. The collection of genotypes included 25 cytoplasmic male sterility ogura and 21 restorer lines (Rfo). The set of genotypes was completed with B. (continued)

      Published: April 15, 2016

    • M. Kathryn Turner, Yue Jin, Matthew N. Rouse and James A. Anderson
      Stem Rust Resistance in ‘Jagger’ Winter Wheat

      ‘Jagger’ has been used widely as a parent to develop hard red winter wheat (Triticum aestivum L.) varieties throughout the US southern Great Plains. Jagger has resistance to the stem rust pathogen race TTTTF, which is virulent to many winter wheat cultivars, yet the genetic basis of this resistance was unknown. Marker analysis and resistance to leaf rust and stripe rust demonstrated that Jagger has the 2NS/2AS translocation from T. ventricosum (Tausch) Ces., Pass. (continued)

      Published: April 15, 2016

    • Mahendra Dia, Todd C. Wehner, Richard Hassell, Daniel S. Price, George E. Boyhan, Stephen Olson, Stephen King, Angela R. Davis and Gregory E. Tolla
      Genotype × Environment Interaction and Stability Analysis for Watermelon Fruit Yield in the United States

      One of the major breeding objectives for watermelon (Citrullus lanatus [Thumb.] Matsum & Nakai) is improved fruit yield. High yielding genotypes have been identified, so we measured their stability for fruit yield and yield components over diverse environments. The objectives of this study were to (i) evaluate the yield of watermelon genotypes over years and locations, (ii) identify genotypes with high stability for yield, and (iii) measure the correlations among univariate and multivariate stability statistics. A diverse set of 40 genotypes was evaluated over 3 yr (2009, 2010, and 2011) and eight locations across the southern United States in replicated trials. (continued)

      Published: April 15, 2016

    • Fan Yan, Shaokang Di, Yoshinori Murai, Tsukasa Iwashina, Toyoaki Anai and Ryoji Takahashi
      New Allelic Variant Discovered at Soybean Flower Color Locus W1 Encoding Flavonoid 3′5′-hydroxylase

      A soybean line producing light purple flowers (E023-H-12) was developed from an ethyl methanesulfonate (EMS)-treated population of cultivar Bay. The objective of this study was to investigate the genetic and molecular basis of flower color variation in E023-H-12. Genetic analysis suggested that the W1 gene encoding a flavonoid 3′5′-hydroxylase (F3′5′H) controls light purple flower color. A single plant with purple flowers was generated in an F2 population derived from a cross between E023-H-12 and Clark-w1 with white flowers, probably because of intragenic recombination of the F35H gene. (continued)

      Published: April 15, 2016

    • Xiuting Zheng, Kevin A. Hoegenauer, Jose Quintana, Alois A. Bell, Amanda M. Hulse-Kemp, Robert L. Nichols and David M. Stelly
      SNP-Based MAS in Cotton under Depressed-Recombination for Ren lon –Flanking Recombinants: Results and Inferences on Wide-Cross Breeding Strategies

      Strong resistance to reniform nematode (Rotylenchulus reniformis) was previously introgressed from the F-genome diploid species Gossypium longicalyx (2n = 2x = 26) into Upland cotton (G. hirsutum L., 2n = 4x = 52, 2[AD]1), and attributed to the gene Renlon. Two resistant elite lines were released, but their seedlings are differentially stunted in nematode-infested fields. Here, we report on the development of linked SNPs and their use to disrupt “linkage drag” around Renlon. (continued)

      Published: April 8, 2016

    • Vijay Chaikam, Leocadio Martinez, Albrecht E. Melchinger, Wolfgang Schipprack and Prasanna M. Boddupalli
      Development and Validation of Red Root Marker-Based Haploid Inducers in Maize

      One of the critical limitations for the in vivo production of doubled haploid (DH) lines in maize (Zea mays L.) is the inability to effectively identify haploids in a significant proportion of induction crosses due to the possibility of complete or partial inhibition of the currently used R1-nj (Navajo) color marker. In this study, we demonstrate that the R1-nj marker could result in a high proportion of false positives among the haploids identified, besides being ineffective in germplasm with natural anthocyanin expression in pericarp tissue. To address these limitations, we developed haploid inducer lines with triple anthocyanin color markers, including the expression of anthocyanin coloration in the seedling roots and leaf sheaths, in addition to the Navajo marker on the seed. Although these inducers show acceptable haploid induction rates ranging from 8.6 to 10.2%, they exhibited relatively poor agronomic performance compared with tropicalized haploid inducers within tropical environments. (continued)

      Published: April 8, 2016

    • Diego Jarquín, Sergio Pérez-Elizalde, Juan Burgueño and José Crossa
      A Hierarchical Bayesian Estimation Model for Multienvironment Plant Breeding Trials in Successive Years

      In agriculture and plant breeding, multienvironment trials over multiple years are conducted to evaluate and predict genotypic performance under different environmental conditions and to analyze, study, and interpret genotype × environment interaction (G × E). In this study, we propose a hierarchical Bayesian formulation of a linear–bilinear model, where the conditional conjugate prior for the bilinear (multiplicative) G × E term is the matrix von Mises–Fisher (mVMF) distribution (with environments and sites defined as synonymous). A hierarchical normal structure is assumed for linear effects of sites, and priors for precision parameters are assumed to follow gamma distributions. Bivariate highest posterior density (HPD) regions for the posterior multiplicative components of the interaction are shown within the usual biplots. (continued)

      Published: February 12, 2016


    • Michelle J. Serapiglia, Akwasi A. Boateng, D.K. Lee and Michael D. Casler
      Switchgrass Harvest Time Management Can Impact Biomass Yield and Nutrient Content

      Switchgrass (Panicum virgatum L.) is a dedicated energy crop native to tallgrass prairie and savanna ecosystems of North America. Although high biomass yield is of significant importance for the development of switchgrass as a bioenergy crop, mineral nutrients in biomass are critically important for sustainable bioenergy crop production but are detrimental for thermochemical conversion of biomass to energy. To evaluate biomass yield and nutrient uptake or nutrient cycling in switchgrass cultivars, replicated trials across three sites (Arlington, WI; Marshfield, WI; and Urbana, IL) were established in 2009. The switchgrass cultivars were harvested once annually at upland peak, after killing frost, or post-winter in the spring from 2010 to 2014. (continued)

      Published: April 29, 2016

    • Lena D. Syrovy, Steven J. Shirtliffe and Mark E. Zarnstorff
      Yield Response to Early Defoliation in Spring-Planted Canola

      Canola (Brassica napus L.) is a high-value summer annual crop grown in the northern Great Plains of Canada and the United States. During the early stages of its life, the crop may lose leaf area as a result of spring hail storms, frost, herbicides, animal grazing, and insects. However, little information is available on the effect of defoliation during vegetative growth on yield for spring-planted canola. To address this gap, a five site-year study was conducted in central Saskatchewan, Canada, to test canola recovery from partial (50%) or full (100%) defoliation at five stages before flowering (2-, 4-, 6-, 8-, and 10-leaf stages). (continued)

      Published: April 15, 2016


    • Bandara Gajanayake and K. Raja Reddy
      Sweetpotato Responses to Mid- and Late-Season Soil Moisture Deficits

      Soil moisture-dependent, quantitative information on sweetpotato [Ipomoea batatas L. (Lam)] plant processes is vital for crop management and modeling because of the projected shrinking and uneven distributions of rainfall and irrigation water supply due to climate change. This study was conducted to quantify the growth, physiology, biomass, and storage root yield responses of sweetpotato under four evapotranspiration-based irrigation treatments (100, 60, 40, and 20% ET) in sunlit growth chambers. Irrigation treatments were imposed from 41 to 97 d after transplanting. (continued)

      Published: April 29, 2016


    • R. Howard Skinner and Curtis J. Dell
      Yield and Soil Carbon Sequestration in Grazed Pastures Sown with Two or Five Forage Species

      Increasing plant species richness is often associated with an increase in productivity and associated ecosystem services such as soil C sequestration. Here we report on a 9-yr experiment to evaluate the forage production and C sequestration potential of grazed pastures sown to either a two-species cool-season grass-legume mixture or a five-species mixture of grasses, legumes, and a non-legume forb. We hypothesized that forage production and soil C sequestration would be greater in the five-species compared with the two-species mixture. We also evaluated the effects of rainfall and temperature on the difference in forage production between mixtures. (continued)

      Published: April 29, 2016

    • Valdson J. Silva, Carlos G.S. Pedreira, Lynn E. Sollenberger, Liliane S. Silva, Júnior I. Yasuoka and Ianê C.L. Almeida
      Canopy Height and Nitrogen Affect Herbage Accumulation, Nutritive Value, and Grazing Efficiency of ‘Mulato II’ Brachiariagrass

      Brachiaria sp. grasses are widely used in planted pastures in Brazil. ‘Mulato II’ is a productive Brachiaria hybrid (B. ruziziensis × B. (continued)

      Published: April 29, 2016

    • R. Howard Skinner and Sarah C. Goslee
      Defoliation Effects on Pasture Photosynthesis and Respiration

      Ecosystem C gain or loss from managed grasslands depends on management practices. However, limited information is available at the field scale on how the type of defoliation, specifically grazing vs. cutting, affects gross primary productivity (GPP) and ecosystem respiration (RE) immediately after defoliation and during the regrowth process. This study takes advantage of daily field-scale micrometeorological measurements of GPP and RE made over a 9-yr period on two pastures that were grazed or cut approximately five times per year to examine the relative effects of grazing and cutting on GPP and RE. (continued)

      Published: April 15, 2016


    • E.A. Lee, W. Deen, M.E. Hooyer, A. Chambers, G. Parkin, R. Gordon and A.K. Singh
      Involvement of Year-to-Year Variation in Thermal Time, Solar Radiation and Soil Available Moisture in Genotype-by-Environment Effects in Maize

      Year-to-year variability in temperature, precipitation, and solar radiation is increasing due to global climate change. This enhanced variation will likely lead to more frequent and larger genotype-by-environment interaction (G × E) effects impacting genetic gains from selection. In this study G × E effects are examined in the absence of genetic variation for thermal time requirements (i.e., phenology), with an understanding of which physiological mechanisms are responsible for genotypic differences in grain yield, using a series of developmental windows, and in the context of fully characterized environments. Using a set of hybrid RILs of the classic Iodent × Stiff Stalk heterotic pattern, we demonstrate that the hybrid RILs are phenologically uniform and that grain yield differences are due primarily to genetic variation in dry matter accumulation during the grain filling period. (continued)

      Published: February 12, 2016


    • Jessica L. Shoup Rupp, Luisa F. Cruz, Harold N. Trick and John P. Fellers
      RNAi-Mediated, Stable Resistance to Triticum mosaic virus in Wheat

      Triticum mosaic virus (TriMV) was discovered in 2006 and affects wheat (Triticum spp.) production systems in the Great Plains of the United States. Genetic resistance is available in a few commercial varieties; however, it is not effective above 20°C. RNA interference (RNAi) was evaluated as an alternative strategy to generate resistance to TriMV. An RNAi pANDA-mini-based hairpin expression vector was created from 272 bp of the TriMV coat protein (CP) sequence. (continued)

      Published: April 22, 2016

    • Xiaojie Zhao, Xuke Lu, Zujun Yin, Delong Wang, Junjuan Wang, Weili Fan, Shuai Wang, Tianbao Zhang and Wuwei Ye
      Genome-wide Identification and Structural Analysis of Pyrophosphatase Gene Family in Cotton

      Pyrophosphatase is a hydrolytic enzyme that utilizes pyrophosphate as a substrate. H+-PPase, an important proton pump on the vacuolar membrane, plays an important role in regulating cell expansion, H+ electrochemical gradient, and secondary active transport of inorganic ions, organic acids and saccharides. Under low temperature, drought, high NaCl concentration, and hypoxia, H+-PPase gene expression is promoted to maintain the intracellular balance and enhance the ability of stress resistance in plants. The GhVP gene family is a class of H+-PPase genes in Gossypium hirsutum L. (continued)

      Published: April 15, 2016

    • Scott L. McClinchey, J. Brent Gillespie, Tracey L. Fisher, Kerry Taylor, Mary Challender and Daria H. Schmidt
      Quality Characteristics of Glyphosate-Tolerant Canola Cultivars Containing a Glyphosate Acetyltransferase Transgene (Event DP-Ø73496-4)

      Canola (Brassica napus L.) was transformed with an insert that expresses the GAT4621 protein, conferring tolerance to the nonselective herbicidal ingredient glyphosate. Event DP-Ø73496-4 (trade name Optimum GLY Canola) was introgressed into additional female inbred genetic backgrounds and hybrid seed lots were created to evaluate canola quality characteristics for cultivar registration in Canada. Field trials were conducted in 2012 and 2013 across several locations in appropriate maturity zones for the cultivars. Results indicated no difference for key canola quality parameters across genetic backgrounds and locations. (continued)

      Published: April 15, 2016


    • Shelley H. Jansky, Amy O. Charkowski, David S. Douches, Gabe Gusmini, Craig Richael, Paul C. Bethke, David M. Spooner, Richard G. Novy, Hielke De Jong, Walter S. De Jong, John B. Bamberg, A. L. Thompson, Benoit Bizimungu, David G. Holm, Chuck R. Brown, Kathleen G. Haynes, Vidyasagar R. Sathuvalli, Richard E. Veilleux, J. Creighton Miller, Jim M. Bradeen and Jiming M. Jiang
      Reinventing Potato as a Diploid Inbred Line–Based Crop

      The third most important food crop worldwide, potato (Solanum tuberosum L.) is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, that the creation of inbred potato is not feasible, and that propagation by seed tubers is ideal. In this paper, we question those assumptions and propose to convert potato into a diploid inbred line–based crop propagated by true seed. (continued)

      Published: April 15, 2016


    • Mizan Tesfay Abraha, Hussein Shimelis, Mark Laing and Kebebew Assefa
      Performance of Tef [ Eragrostis tef (Zucc.) Trotter] Genotypes for Yield and Yield Components Under Drought-Stressed and Non-Stressed Conditions

      Tef [Eragrostis tef (Zucc.) Trotter] is a staple food crop in Ethiopia, and has become known globally as a health food for its gluten-free flour, which also has a unique nutritional profile. A key to successful variety development through designed breeding is the use of diverse genetic resources, especially when breeding for complex traits such as tolerance to drought stress. The objective of this study was to assess the response of genetically diverse populations of tef genotypes for yield and yield components, with special emphasis on drought-stress tolerance, to select promising parents for breeding. One hundred forty-four tef genotypes were evaluated, involving four experiments representing optimum moisture and drought-stressed environments. (continued)

      Published: April 15, 2016


    • Stephen Smith, Sergio Lence, Dermot Hayes, Julian Alston and Eloy Corona
      Elements of Intellectual Property Protection in Plant Breeding and Biotechnology: Interactions and Outcomes

      Public and private investments in plant breeding have a proven track record of increasing agricultural productivity, significantly contributing to economic well-being or social welfare. Substantial investments in research and development are required before a new plant variety can be developed and released, which the private sector can only recoup through commercial sales coupled with property rights. We previously published outcomes from economic modeling implementing different categories and hypothetical variants of intellectual property protection (IPP) in the field of plant breeding and biotechnology. Our goal here is to portray these outcomes using examples that will be more immediately familiar to the plant-breeding and policy-making communities. (continued)

      Published: April 15, 2016


    • Loren Trimble, Stacie Shuler and William F. Tracy
      Characterization of Five Naturally Occurring Alleles at the Sugary1 Locus for Seed Composition, Seedling Emergence, and Isoamylase1 Activity

      The mutant su1-ref allele is of interest in the commercial sweet maize (Zea mays L.) industry. It was the only starch synthesis mutation used for sweet maize until the 1960s and is still used today, especially in combinations with other loci. The wild-type Su1 allele produces a starch debranching-type isoamylase, ISA1, required for normal amylopectin and starch granule crystal formation in maize endosperm. Five naturally occurring mutant alleles have been identified at the su1 locus, but they have not been characterized for seedling emergence, field traits, mature kernel composition, or ISA1 enzyme activity. (continued)

      Published: April 15, 2016


    • K. Kleinknecht, J. Möhring, F. Laidig, U. Meyer and H.P. Piepho
      A Simulation-Based Approach for Evaluating the Efficiency of Multienvironment Trial Designs

      Plant breeding and official variety testing involve the challenge to design multienvironmental trials in several years and locations. Several variables influence the performance and, therefore, the possible selection gain of such trials. We provide a simulation-based approach using SAS to vary these variables and to allow a comparison of different scenarios for the design of series of trials regarding selection gain. Our approach builds on the FORTRAN software tool SELSYS. (continued)

      Published: March 11, 2016

    • Mark Cooper, Frank Technow, Carlos Messina, Carla Gho and L. Radu Totir
      Use of Crop Growth Models with Whole-Genome Prediction: Application to a Maize Multienvironment Trial

      High throughput genotyping, phenotyping, and envirotyping applied within plant breeding multienvironment trials (METs) provide the data foundations for selection and tackling genotype × environment interactions (GEIs) through whole-genome prediction (WGP). Crop growth models (CGM) can be used to enable predictions for yield and other traits for different genotypes and environments within a MET if genetic variation for the influential traits and their responses to environmental variation can be incorporated into the CGM framework. Furthermore, such CGMs can be integrated with WGP to enable whole-genome prediction with crop growth models (CGM-WGP) through use of computational methods such as approximate Bayesian computation. We previously used simulated data sets to demonstrate proof of concept for application of the CGM-WGP methodology to plant breeding METs. (continued)

      Published: February 12, 2016

    • Marcos Malosetti, Daniela Bustos-Korts, Martin P. Boer and Fred A. van Eeuwijk
      Predicting Responses in Multiple Environments: Issues in Relation to Genotype × Environment Interactions

      Prediction of the phenotypes for a set of genotypes across multiple environments is a fundamental task in any plant breeding program. Genomic prediction (GP) can assist selection decisions by combining incomplete phenotypic information over multiple environments (MEs) with dense sets of markers. We compared a range of ME-GP models differing in the way environment-specific genetic effects were modeled. Information among environments was shared either implicitly via the response variable, or by the introduction of explicit environmental covariables. (continued)

      Published: February 5, 2016

    • Bettina Lado, Pablo González Barrios, Martín Quincke, Paula Silva and Lucía Gutiérrez
      Modeling Genotype × Environment Interaction for Genomic Selection with Unbalanced Data from a Wheat Breeding Program

      Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there is not a clear strategy on how to incorporate genotype × environment interaction (GEI) to GS models. Increased prediction accuracy could be achieved using mixed models to exploit GEI by borrowing information from other environments. The objective of this work was to compare strategies to exploit GEI in GS using mixed models. (continued)

      Published: January 29, 2016

    • Jakub Paderewski, Hugh G. Gauch, Wieslaw Mądry and Edward Gacek
      AMMI Analysis of Four-Way Genotype × Location × Management × Year Data from a Wheat Trial in Poland

      Grain yield data of winter wheat (Triticum aestivum L.) trials in Poland had a four-way factorial design of 24 genotypes by 20 locations by two managements by 3 yr. The experimental design had genotype–management strip plots with two replications for genotypes, with somewhat more genotypes than the 24 having no missing data. The research objectives were to extend additive main effects and multiplicative interactions (AMMI) analysis from two-way to higher-way datasets to reduce spurious complexity originating from noise, delineate wheat mega-environments in Poland, and make genotype recommendations within each mega-environment. Statistical analysis began with adjusting the yield estimates using the strip-plot experimental design and then combining the results in a genotype × location × management × year (GLMY) table. (continued)

      Published: September 25, 2015

    • Weikai Yan
      Analysis and Handling of G × E in a Practical Breeding Program

      Genotype by environment interaction (GE) is a reality in plant breeding and crop production, and has to be dealt with. There are but two viable options to deal with GE: to utilize it or to avoid it, depending on whether it is repeatable. Repeatable GE can be selected for (utilized) whereas unrepeatable GE has to be selected against (avoided). To utilize GE involves identifying repeatable GE, dividing the target region into subregions or megaenvironments (ME) based on the repeatable GE pattern, and selecting within ME. (continued)

      Published: December 3, 2015

    • José Crossa, Gustavo de los Campos, Marco Maccaferri, Roberto Tuberosa, J. Burgueño and Paulino Pérez-Rodríguez
      Extending the Marker × Environment Interaction Model for Genomic-Enabled Prediction and Genome-Wide Association Analysis in Durum Wheat

      The marker × environment interaction (M×E) genomic model can be used to generate predictions for untested individuals and identify genomic regions in which effects are stable across environments and others that show environmental specificity. The objectives of this study were (i) to extend the M×E model using priors that produce shrinkage and variable selection such as Bayesian ridge regression (BRR) and BayesB (BB), respectively, and (ii) to evaluate the genomic prediction accuracy of M×E, single-environment, and across-environment models using a multiparental durum wheat (Triticum turgidum L. spp. duram) population characterized for grain yield (GY), grain volume weight (GVW), 1000-kernel weight (GWT), and heading date (HD) in four environments. (continued)

      Published: December 3, 2015

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