Showing papers in "Crop Science in 2006"
TL;DR: A systematic comparison of the Additive Main effects and Multiplicative Interaction model, GGE, and other SVD-based model families is presented, using both statistical theory and empirical investigations, while considering both current practices and best practices.
Abstract: The Additive Main effects and Multiplicative Interaction (AMMI) model, Genotype main effects and Genotype X Environment interaction (GGE) model, and Principal Components Analysis (PCA) are singular value decomposition (SVD) based statistical analyses often applied to yield-trial data. This paper presents a systematic comparison, using both statistical theory and empirical investigations, while considering both current practices and best practices. Agricultural researchers using these analyses face two inevitable choices. First is the choice of a model for visualizing data. AMMI is decidedly superior, not for statistical reasons, but rather for agricultural reasons. AMMI partitions the overall variation into genotype main effects, environment main effects, and genotype X environment interactions. These three sources of variation present agricultural researchers with different challenges and opportunities, so it is best to handle them separately, while still considering all three in an integrated manner. Second is the choice of a member of a given model family for gaining predictive accuracy. AMMI, GGE, and other SVD-based model families are essentially equivalent, but best practices require model diagnosis for each individual dataset to determine which member is most predictively accurate. Making these two choices well allows researchers to extract more usable information from their data, thereby increasing efficiency and accelerating progress.
587 citations
TL;DR: Broadening the conservation circle to establish closer collaborations with grassroots conservation movements and community seed banks is necessary to better conserve the broad range of CGR and as an essential starting point for participatory breeding efforts.
Abstract: Concerns about the genetic erosion of crop genetic resources (CGR) were first articulated by scientists in the mid-20th century and have since become an important part of national policies and international treaties The C-8 (Plant Genetic Resources) section of the Crop Science Society of America (CSSA) was created in 1990 in response to these concerns Over the last 50 yr, both ex situ and in situ conservation have been set up to maintain threatened CGR During this period, a set of tools (core collections, molecular markers, and geographic information systems) has been adopted to facilitate conservation and utilization by breeders Current and future trends include characterization of the genotypic basis of phenotypic variation and the evolutionary, ecological, and human factors that have shaped CGR The intellectual property regime to which CGR are subjected since 1980 has limited the exchange of germplasm It remains to be seen if these regimes will evolve so as to achieve basic goals of conservation of genetic diversity and traditional knowledge associated with diversity, while at the same time reward breeders and farmers Funding of biodiversity conservation remains a critical point Finally, broadening the conservation circle to establish closer collaborations with grassroots conservation movements and community seed banks is necessary to better conserve the broad range of CGR and as an essential starting point for participatory breeding efforts
321 citations
TL;DR: This paper illustrates the use of Proc MIXED of the SAS system to implement REML estimation of genotypic and phenotypic correlations and a method to obtain approximate parametric estimates of the sampling variances of the correlation estimates is presented.
Abstract: Plant breeders traditionally have estimated genotypic and phenotypic correlations between traits using the method of moments on the basis of a multivariate analysis of variance (MANOVA). Drawbacks of using the method of moments to estimate variance and covariance components include the possibility of obtaining estimates outside of parameter bounds, reduced estimation efficiency, and ignorance of the estimators' distributional properties when data are missing. An alternative approach that does not suffer these problems, but depends on the assumption of normally distributed random effects and large sample sizes, is restricted maximum likelihood (REML). This paper illustrates the use of Proc MIXED of the SAS system to implement REML estimation of genotypic and phenotypic correlations. Additionally, a method to obtain approximate parametric estimates of the sampling variances of the correlation estimates is presented. MANOVA and REML methods were compared with a real data set and with simulated data. The simulation study examined the effects of different correlation parameter values, genotypic and environmental sample sizes, and proportion of missing data on Type I and Type II error rates and on accuracy of confidence intervals. The two methods provided similar results when data were balanced or only 5% of data were missing. However, when 15 or 25% data were missing, the REML method generally performed better, resulting in higher power of detection of correlations and more accurate 95% confidence intervals. Samples of at least 75 genotypes and two environments are recommended to obtain accurate confidence intervals using the proposed method.
317 citations
TL;DR: A model to describe the association between markers and genes as conditional probabilities in synthetic populations under recurrent selection is proposed, which can be computed on the basis of assumptions related to the history of the population.
Abstract: Association analysis is a method potentially useful for detection of marker-trait associations based on linkage disequilibrium, but little information is available on the application of this technique to plant breeding populations. With appropriate statistical methods, valid association analysis can be done in plant breeding populations; however, the most significant marker may not be closest to the functional gene. Bias can arise from (i) covariance among markers and QTL, frequently related to population structure or intense selection and (ii) differences in initial frequencies of marker alleles in the population, such that exclusive alleles tend to be in higher association. The potentials and limitations of germplasm bank collections, synthetic populations, and elite germplasm are compared, as experimental materials for association analysis integrated with plant breeding practice. Synthetics offer a favorable balance of power and precision for association analysis and would allow mapping of quantitative traits with increasing resolution through cycles of intermating. A model to describe the association between markers and genes as conditional probabilities in synthetic populations under recurrent selection is proposed, which can be computed on the basis of assumptions related to the history of the population. This model is useful for predicting the potential of different populations for association analysis and forecasting the response to marker-assisted selection.
250 citations
TL;DR: Near infrared radiation (NIR)–based indices gave the highest level of association with biomass production and the higher associations were observed at heading and grainfilling, rather than at booting, and overall, NIR-based indices were more consistent and differentiated biomass more effectively compared to the other indices.
Abstract: Spectral indices as a selection tool in plant breeding could improve genetic gains for different important traits. The objectives of this study were to assess the potential of using spectral reflectance indices (SRI) to estimate genetic variation for in-season biomass production, leaf chlorophyll, and canopy temperature (CT) in wheat (Triticum aestivum L.) under irrigated conditions. Three field experiments, GHIST (15 CIMMYT globally adapted historic genotypes), RILs1 (25 recombinant inbred lines [RILs]), and RILs2 (36 RILs) were conducted under irrigated conditions at the CIMMYT research station in northwest Mexico in three different years. Five SRI were evaluated to differentiate genotypes for biomass production. In general, genotypic variation for all the indices was significant. Near infrared radiation (NIR)–basedindicesgavethehighestlevelsofassociationwithbiomass production and the higher associations were observed at heading and grainfilling, rather than at booting. Overall, NIR-based indices were more consistent and differentiated biomass more effectively compared to the other indices. Indices based on ratio of reflection spectra cor
235 citations
TL;DR: The results confirm the importance of root structure for LP adaptation and highlight the need for a more detailed understanding of root architectural traits for phenotypic as well as marker-aided selection of more P-efficient crops.
Abstract: Low soil P availability is a primary constraint to common bean (Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty-six F5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR-based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy-one RILs were evaluated in the field at high phosphorus (HP) and LP for P accumulation, total root length (RL), specific RL, and plant dry weight (DW), while all 86 RILs were evaluated in a hydroponic system in the greenhouse for tap, basal, total, and specific RL and plant DW. Phosphorus accumulation in the field correlated with root parameters measured in the greenhouse. A total of 26 individual QTLs were identified for P accumulation and associated root characters using composite interval mapping (CIM) analysis. Phosphorus accumulation QTLs often coincided with those for basal root development, thus, basal roots appear to be important in P acquisition. Independent QTLs were identified for basal and taproot development, and for specific RL. Distinct QTLs for greater specific RL had positive, null and negative effects on P accumulation. Our results confirm the importance of root structure for LP adaptation and highlight the need for a more detailed understanding of root architectural traits for phenotypic as well as marker-aided selection of more P-efficient crops.
229 citations
TL;DR: The effectiveness of recurrent selection under drought is confirmed as a means of improving tropical maize source populations for performance under water deficits and to a lesser extent under low N.
Abstract: The objectives of this study were to evaluate direct and correlated responses to recurrent selection for drought tolerance in two CIMMYT maize (Zea mays L.) source germplasm populations, 'DTP1' and 'DTP2', adapted to the lowland and mid-altitude tropics. Selection was primarily based on grain yield, ears per plant, anthesis-silking interval, and leaf senescence under drought. Cycles C 0 , C 3 , and C 6 of DTP1 and C 0 , C 3 , C 5 and C 9 of DTP2 were evaluated under drought, low N, and optimal conditions. In both populations, significant yield gains were observed under drought conditions, associated with a significant increase in numbers of ears per plant and grains per ear, and significant reductions in anthesis-silking interval, ovule number and abortion rate during grain filling. Abortion rate was positively correlated with the number of ovules at silking and with anthesis-silking interval. In DTP1, recurrent selection under drought was associated with a derease of tassel and stem dry weight and with an increase of ear dry weight and harvest index. This study confirms the effectiveness of recurrent selection under drought as a means of improving tropical maize source populations for performance under water deficits and to a lesser extent under low N. The primary mechanism underlying these changes appears to be improved partitioning of assimilates to the ear at flowering, at the expense of tassel and stem growth.
223 citations
TL;DR: Evidence that genome duplication in crop plants provides genome buffering, increased allelic diversity and heterozygosity, and permits novel phenotypic variation to be generated is reviewed and discussed.
Abstract: All crop plants are polyploid and some genomes have been duplicated more recently than others. Advancements in cytogenetic and molecular tools, including high-density genetic mapping, fl orescent in situ hybridization, and genome and EST sequencing, have enabled new insights into genome composition and the history of genome duplications in crop plants. We review this evidence and discuss the relevance of genome duplication to crop improvement. Polyploidy provides genome buffering, increased allelic diversity and heterozygosity, and permits novel phenotypic variation to be generated. Polyploid formation is often accompanied with loss of duplicated chromatin, changes in gene expression, novel epistatic interactions, and endosperm effects. All of these factors need be considered in a genome-wide context for optimizing marker assisted selection and crop plant improvement. Abbreviations: Ks, synonymous sites; FLC, FLOWERING LOCUS C.
215 citations
TL;DR: Postanthesis maximum WSC content was highly correlated with the amount of WSC mobilized in different internodes, and could be used as a selection criterion to stabilize grain yield under stressful environments.
Abstract: Grain filling in wheat crops grown in semiarid regions may depend more on stored water-soluble carbohydrates (WSC) than on current photosynthesis. We evaluated the hypothesis that intemode WSC content, specific content (WSC content/internode length), and concentration (WSC content/internode weight) of genotypes affect accumulation and mobilization of stem WSC. Genotypic variation for internode WSC-related traits was measured on the main stem at 10-d intervals in 11 diverse wheats grown under well-watered and droughted field conditions across 2 yr. Relationships among internode WSC-related traits were determined. Date of harvest was the most important factor affecting internode WSC-related traits followed by genotype, irrigation, and year. Genotype × date of harvest was the most important interaction. Drought reduced WSC content, specific content, and concentration in different internodes, except WSC concentration in peduncles. Mobilized WSC from peduncle, penultimate, and lower internodes ranged from 70 to 244 mg, from 95 to 227 mg, and from 175 to 450 mg, respectively. The lower internodes provided 51% of the stem mobilized WSC. Mobilized WSC was higher in well-watered than in droughted conditions for penultimate (164 vs. 135 mg) and lower internodes (274 vs. 244 mg). Drought improved mobilization efficiency in the peduncle, penultimate, and lower internodes by 33, 17, and 11%, respectively. Postanthesis maximum WSC content was highly correlated (r = 0.89 to 0.99) with the amount of WSC mobilized in different internodes, and could be used as a selection criterion to stabilize grain yield under stressful environments.
207 citations
TL;DR: Results indicated that a single dominant gene named Rag1 controlled resistance in Dowling, and the monogenic dominant nature of resistance will enable breeders to rapidly convert existing susceptible cultivars to resistant cultivars using backcrossing procedures.
Abstract: The soybean aphid (Aphis glycines Matsumura), a new pest of soybean [Glycine max (L.) Merr.], rapidly spread throughout North America after its arrival in 2000 and caused millions of dollars in economic losses. At present, the application of insecticides is the only means to control the soybean aphid. However, genetic resistance to the aphid was recently discovered in soybean germplasm and the soybean cultivar Dowling was identified as having strong antibiosis-type aphid resistance. The objective of this study was to determine the inheritance of resistance to the soybean aphid in Dowling. Resistance in F1 ,F 2, and F2–derived F3 (F2:3) families from crosses between Dowling and the two susceptible soybean cultivars Loda and Williams 82 was analyzed. All F1 plants were resistant to the aphid. Heterogeneity of segregation of F2 plants in 14 Dowling 3 Loda F2 families was nonsignificant (P 5 0.16), and pooled F2 data, with 132 resistant to 45 susceptible plants, fit a 3:1 ratio (P 5 0.90). F2 plants from Dowling 3 Williams 82 segregated 135 resistant to 44 susceptible, also fitting a 3:1 ratio (P 5 0.89). Segregation among the F2:3 families fit a 1:2:1 monogenic inheritance pattern. These results indicated that a single dominant gene named Rag1 controlled resistance in Dowling. The monogenic dominant nature of resistance will enable breeders to rapidly convert existing susceptible cultivars to resistant cultivars using backcrossing procedures.
203 citations
TL;DR: NIR-based indices were more consistent and differentiated grain yield more effectively compared to the other indices, and near infrared radiation (NIR)–based indices gave the highest levels of association with grain yield during the 3 yr of the study.
Abstract: The objectives of this study were to assess the potential of using spectral reflectance indices (SRI) as an indirect selection tool to differentiate spring wheat (Triticum aestivum L.) genotypes for grain yield under irrigated conditions. This paper demonstrates only the first step in using the SRI as indirect selection criteria by reporting genetic variation for SRI among genotypes, the effect of phenology and year on SRI and their interaction with genotypes, and the correlations between SRI and grain yield and yield components of wheat. Three field experiments—15 CIMMYT globally adapted genotypes (GHIST), 25 random F3–derived lines (RLs1), and 36 random F3–derived lines (RLs2)—were conducted under irrigated conditions at the CIMMYT research station in northwest Mexico in three different years. Five previously developed SRI (photochemical reflectance index [PRI], water index [WI], red normalized difference vegetation index [RNDVI], green normalized difference vegetation index [GNDVI], simple ratio [SR]) and two newly calculated SRI (normalized water index-1 [NWI-1] and normalized water index-2 [NWI-2]) were evaluated in the experiments. In general, genotypic variation for all the indices was significant. Near infrared radiation (NIR)–based indices (WI, NWI-1, NWI-2) gave the highest levels of association with grain yield during the 3 yr of the study. A clear trend for higher association between grain yield and the NIR-based indices was observed at heading and grainfilling than at booting. Overall, NIR-based indices were more consistent and differentiated grain yield more effectively compared to the other indices. The results demonstrated the potential of using SRI as a tool in breeding programs for selecting for increased genetic gains for yield.
TL;DR: The objectives were to gain understanding of this protected germplasm by utilizing pedigree information available in the U.S. Patent and PVPA records to enhance the use of this germplas in new line development as the lines become publicly available.
Abstract: Current corn (Zea mays L.) hybrids are produced using proprietary
inbred lines as parents. These proprietary lines are protected by U.S.
Patent and/or the U.S. Plant Variety Protection Act (PVPA) and their
use is restricted, but as protection expires these lines become available
to the entire corn breeding industry. Our objectives were to gain understanding
of this protected germplasm by utilizing pedigree information
available in the U.S. Patent and PVPA records to enhance the
use of this germplasm in new line development as the lines become
publicly available. Ownership, derivation, and lineage of corn inbred
lines protected by U.S. Patent or PVPA from 1980 to 2004 were surveyed.
Thirty-three companies have protected 908 corn inbred lines and
four of these companies: Dekalb Genetics (DK), Holden’s Foundation
Seeds (LH), Pioneer Hi-Bred (PH), and Syngenta (SG) originated 685
of them.We identified the most significant lines by their cumulative use
as parents in the development of new lines. Much of today’s germplasm
originates from seven progenitor lines: B73, LH82, LH123, PH207,
PH595, PHG39, and Mo17. The germplasm surveyed is grouped by
pedigree lineage into Oh43, Lancaster, Oh07-Midland, Iodent, Stiff
Stalk, Commercial hybrid derived, and Argentine Maiz Amargo backgrounds,
with new diversity emerging from the two latter groups. Recycling
elite inbred lines using two-parent crosses followed by pedigree
breeding was the most prevalent method of new line development.
TL;DR: Harvesting long-established switchgrass stands once per year after a killing frost and applying N at 56 kg ha -1 was an effective system for switchgrass biomass production and persistence on land enrolled in or managed similarly to CRP in South Dakota.
Abstract: Switchgrass (Panicum virgatum L.) has been planted on land enrolled in the Conservation Reserve Program (CRP). Management strategies for conversion of this land from CRP to biomass energy require evaluation. Objectives of this study were to: (i) determine the effect of harvest timing and N rate on biomass production and characteristics of switchgrass land enrolled in or managed similarly to CRP and (ii) evaluate the impact of harvest management on species composition and persistence. Five N rates (spring applications of 0, 56, 112, and 224 kg ha -1 and 224 kg ha -1 split between spring and postharvest) and two harvest timings (anthesis and post-killing frost) were applied to plots from 2001 to 2003 at three South Dakota locations. Harvesting after a killing frost produced higher total yields and improved switchgrass persistence compared with anthesis harvests. The concentration of neutral detergent fiber (NDF), add detergent fiber (ADF), and add detergent lignin (ADL) increased between anthesis and killing-frost harvests, while total nitrogen (TN) and ash decreased. Nitrogen applied at 56 kg ha -1 increased total biomass without affecting switchgrass persistence, but there was no additional benefit with N above 56 kg ha -1 . Harvesting long-established switchgrass stands once per year after a killing frost and applying N at 56 kg ha -1 was an effective system for switchgrass biomass production and persistence on land enrolled in or managed similarly to CRP in South Dakota.
TL;DR: The results of principal component (PC) analysis and correlation analysis of nonparametric stability statistics and yield indicated that only rank-sum and TOP methods would be useful for simultaneously selecting for high yield and stability.
Abstract: Analysis of multienvironment trials (METs) of crops for cultivar evaluation and recommendation is an important issue in plant breeding research. Evaluating both stability of performance and high yield is essential in MET analyses. The objective of this investigation was to compare 10 nonparametric stability methods and apply nonparametric tests (which do not require distributional assumptions) for genotype-by-environment (G X E) interaction to 11 lentil (Lens culinaris Medik) genotypes. Nine improved lentil genotypes and two local cultivars were grown in 20 semiarid environments in Iran from 2002 to 2004. Results of nonparametric tests of G X E interaction and a combined ANOVA across environments showed there were both crossover and noncrossover G × E interactions and genotypes varied significantly for yield. In this study, high values of TOP (proportion of environments in which a genotype ranked in the top third) and low values of rank-sum (sum of ranks of mean yield and Shukla's stability variance) were associated with high mean yield, but the other nonparametric methods were not positively correlated with mean yield and instead characterized a static concept of stability. The results of principal component (PC) analysis and correlation analysis of nonparametric stability statistics and yield indicated that only rank-sum and TOP methods would be useful for simultaneously selecting for high yield and stability. These methods recommended FLIP 92-12L as stable and FLIP96-6L as unstable genotypes. A biplot of the first two PCs also revealed that the nonparametric methods grouped as three distinct classes that corresponded to different agronomic and biological concepts of stability.
TL;DR: Minimizing the exposure of chickpea to high temperature stress during pod development will increase pod fertility, seed set, and seed yield of the crop.
Abstract: Minimizing the exposure of an annual crop to abiotic stresses may increase seed yield. A study was conducted to determine the effect of high temperature stress during reproductive development on pod fertility, seed set, and seed yield of chickpea (Cicer arietinum L). ‘Myles’ desi and ‘Xena’ kabuli chickpea were grown in a controlled environment under 20/16°C day/night air temperatures (control). High (35/16°C) and moderate (28/16°C) temperature stresses were imposed for 10 d during early flowering and pod development. Compared to the control, the early flower high temperature stress decreased (P < 0.01) pod production by 34% for Myles and 22% for Xena, whereas high temperature stress during pod development decreased (P < 0.05) seeds per plant by 33% for Myles and 39% for Xena. Consequently, the high temperature stress during pod development decreased (P < 0.01) seed yield by 59% for Myles and 53% for Xena. Yield reduction was greater due to the stress during pod development compared to the stress during early flowering. Plants recovered to a greater degree from the early flower stress compared to the pod development stress. The Myles desi produced 40 seeds per plant and the Xena kabuli produced 15 seeds per plant, whereas the Myles had smaller individual seed size than the Xena. Consequently, the Myles desi produced 26% greater seed yield than the Xena kabuli under the same conditions. Minimizing the exposure of chickpea to high temperature stress during pod development will increase pod fertility, seed set, and seed yield of the crop.
TL;DR: Drought resistant genotypes should be used for determining irrigation frequency,amount ofwatertobe applied, andMechanism sofresistance and for identifying, mapping, and pyramiding favorable genes for dryland and irrigation-assisted sustainable production systems.
Abstract: Drought is a worldwide constraint to dry bean (Phaseolus vulgaris L.) production. The objective of this research was to determine the response of three dry bean landraces and 13 cultivars evaluated under non-stressed (NS) and intermittent drought-stressed (DS) environments at Kimberly, Idaho in 2003 and 2004. The NS received seven irrigations in 2003 and five in 2004, and DS only four in 2003 and two in 2004. Most water use occurred within the top 0.5 m soil in both the NS and DS. Drought reduced biomass and seed yield, harvest index, and seedweight. Maturitywas delayedin severe drought,butwassimilar or shortened by 1 to 6 d under moderate drought. Mean seed yield was reduced by 62% in 2003 and by 27% in 2004. Common Red Mexican and CO 46348 had high seed yield in both NS and DS environments, whereas ‘Matterhorn’ and ‘Othello’ yielded comparatively high under DS but moderately in NS environment. Drought resistance was inadvertently reduced from Common Red Mexican landrace to intermediate levels in ‘NW-63’ and ‘UI 239’ released in 1979 and 1993, respectively, andmore recently released ‘LeBaron’ (1999) and ‘UI 259’ (1996)weresusceptible.Conversely,droughtresistancewasincreasedin newer pinto (Othello 1986; CO 46348) and great northern (Matterhorn 1998) releases compared to the landraces and older cultivars tested for thosemarketclasses.SeedyieldinNSandDSwaspositivelycorrelated. Seed yield was also correlated with harvest index in DS and NS. All early maturing cultivars except Othello (e.g., UI 59, US 1140, Common Pinto, Topaz, UI 320, and LeBaron) were susceptible. Common Red Mexicandidnothaveanyreductioninseedweightduetodroughtstress. Drought resistant genotypes should be used for determining irrigation frequency,amountofwatertobeapplied,andmechanismsofresistance and for identifying, mapping, and pyramiding favorable genes for dryland and irrigation-assisted sustainable production systems.
TL;DR: Indirect selection on these two traits was predicted to be efficient for improving yield under weed competition and weed-suppressive ability of aerobic rice.
Abstract: Forty rice (Oryza sativa L.) cultivars and breeding lines used in the International Rice Research Institute (IRRI) upland rice breeding program were evaluated in adjacent weed-free and weedy trials in aerobic soil conditions during the wet seasons of 2001, 2002, and 2003. The objectives of this study were to investigate genetic variability in weed suppression and yield and to identify traits that could be used as selection criteria for improved weed competitiveness. Correlations among and heritability (H) of agronomic traits and early vigor were estimated in weedy and weed-free trials. Regression analysis was performed to predict weedy yield and weed biomass. Cultivars differed widely in the growth of weed biomass they permitted (126?296 g m?2) and in yield under competition (0.5?2.5 Mg ha?1). Cultivar yield, duration, biomass, harvest index, height, and vegetative vigor under weed-free conditions were closely correlated with the same traits measured under weedy conditions. Weedy yield and weed biomass were both moderately heritable (H = 0.55 and 0.38 for means estimated from single-year, three replicate trial, respectively) and genetically correlated with each other (r = ?0.84). Weed-free yield and vigor at two weeks after seeding (WAS) were moderately heritable (H = 0.68 and 0.38 for means estimated from a single-year, three replicate trial, respectively) and were highly genetically correlated with weedy yield (r = 1.00 and 0.88, respectively) and weed biomass (r = ?0.89 and ?0.67, respectively). Vegetative vigor at two WAS and grain yield measured under weed-free conditions explained a combined 87% of cultivar variation in weedy yield and 40% in weed biomass. Indirect selection on these two traits was predicted to be efficient for improving yield under weed competition and weed-suppressive ability of aerobic rice.
TL;DR: Balanced partitioning of stem length into upper and lower internodes and internode maximum specific weight are important in genotypic accumulation and mobilization of stem reserves in wheat.
Abstract: Wheat crops grown in dryland areas may depend more on stem reserves for grain filling than on current photosynthesis. We evaluated the hypothesis that internode length, weight, and specific weight of genotypes affect accumulation and mobilization of stem reserves. This knowledge might complement selection in stressful environments. Genotypic variation for internode characteristics and their effects on dry matter accumulation and mobilization were measured at 10-d intervals in 11 diverse wheat cultivars grown under well-watered and droughted field conditions across 2 yr. Relationships among internode characteristics and accumulation and mobilization of stem reserves were determined. The main effect of year, irrigation, genotype, and harvest date and genotype x harvest date interaction were significant. Internode length, weight, and specific weight were reduced under drought. Mobilized dry matter from peduncle, penultimate, and the lower internodes ranged from 43 to 171, 81 to 272, and from 198 to 474 mg, respectively. Mobilized dry matter was less in well-watered than in droughted conditions for peduncle (93 vs. 110 mg) but not for penultimate (173 vs. 143 mg) and the lower internodes (331 vs. 304 mg). Drought increased mobilization efficiency, expressed as percentage of maximum dry mater mobilized, in the peduncle, penultimate, and the lower internodes by 65, 11, and 5%, respectively. Stem maximum specific weight was correlated (r = 0.64) with stem mobilized dry matter. Balanced partitioning of stem length into upper and lower internodes and internode maximum specific weight are important in genotypic accumulation and mobilization of stem reserves in wheat.
TL;DR: It is concluded that adventitious rooting under low phosphorus is a feasible target for bean breeding because recombinant inbred line (RILs) differ substantially in biomass allocation for adventitious roots.
Abstract: Low phosphorus availability is a primary constraint to crop production in developing countries. Adventitious roots play an important role in phosphorus acquisition, as they are localized near the soil surface where phosphorus is relatively abundant A population of recombinant inbred lines of Phaseolus vulgaris L. (G2333/G19839) was screened under high- and low-phosphorus conditions in the greenhouse and field. We observed phenotypic variation and transgressive segregation for adventitious root traits in both environments. Allomctric analysis revealed that although the taproot and basal roots are closely linked to shoot growth, recombinant inbred line (RILs) differ substantially in biomass allocation for adventitious roots. A linkage map with 149 genetic markers and a total cumulative map length of 1175 cM was used to identify a total of 19 QTL across 8 of the 11 linkage groups. Together these quantitative trait lod (QTL) accounted for 19 to 61% of the total phenotypic variation for adventitious root traits in the field and 18 to 39% under greenhouse conditions. Two major QTL for adventitious rooting under low phosphorus conditions in the field were observed on linkage groups B2 and B9 that together accounted for 61% of the observed phenotypic variation. We conclude that adventitious rooting under low phosphorus is a feasible target for bean breeding.
TL;DR: In this paper, the present invention relates to compositions and methods for providing aphid resistance in plants, more particularly, compositions and method for using aphid resistant germplasm for breeding soybean resistant soybean plants.
Abstract: The present invention relates to compositions and methods for providing aphid resistance in plants. More particularly, the invention relates to compositions and methods for using aphid resistant germplasm for breeding soybean aphid resistant soybean plants, including but not limited to cultivars, varieties, lines and methods of breeding the same for commercial use, the breeding methods further involving identifying and using genetic markers for aphid resistant traits.
TL;DR: The origin of U.S. Corn Belt corn, the origins of Northern Flint and Southern Dent races of corn, and how corn hybridization was preceded and eased by hybrid species of the horse (Equus spp.) are reviewed.
Abstract: The origin of U.S. Corn Belt corn (Zea mays L.), heterotic groups, and heterotic patterns becomes less obvious with more cycles of breeding. Heterosis is poorly understood; simple curiosity cries out for more information. I endeavor to shed light on the effect of adaptedness and heterosis on U.S. Corn Belt corn. I relate pertinent happenings in the phenomenal increase in U.S. corn production. I briefly review the origins of Northern Flint and Southern Dent races of corn and two major, persistent open-pollinated cultivars; and how corn hybridization was preceded and eased by hybrid species of the horse (Equus spp.). I discuss heterotic groups and patterns. The objective of U.S. corn breeding has been to adapt a tropical crop to a temperate climate. Adaptedness is important. Open-pollinated cultivars emphasized local adaptation, but some cultivars were more popular, widely grown, and better adapted over a broad geographic region. Hybrid seed corn companies grew larger by selling more widely adapted hybrids that favored germplasm from the more popular, widely grown, better adapted open-pollinated cultivars containing more genes for adaptedness. I examine morphological differences between inbred parents of a widely adapted hybrid. Relatively constant percentage of heterosis of well-adapted hybrids over years is due to seasonal climate affecting hybrids and their parent inbreds in a like manner because of their selection for adaptedness. Adaptedness has been more important than heterosis in the U.S. corn yield and production increases. Adaptedness in analogous heterotic species hybrids of the genus Equus, where body size is female dominant, apparently discriminates for body size between mules and hinnies that have virtually identical genotypes—adaptedness determines superiority over and above heterosis.
TL;DR: The results ratify TRAP as a potentially useful marker technique for genetic diversity studies in sugarcane and reveal homology with known gene sequences from other grass species including Sorghum.
Abstract: Target region amplification polymorphism (TRAP) is a fairly new PCR-based molecular marker technique which uses gene-based information for primer design. The objective of this study was to evaluate the utility of TRAP markers for assessing genetic diversity and interrelationships in sugarcane germplasm collections. Thirty genotypes from the genera Saccharum, Miscanthus, and Erianthus were used in the study. Among the genus Saccharum were the species, S. officinarum L., S. barberi Jesw., S. sinense Roxb., S. spontaneum L., S. robustum Brandes and Jeswiet ex Grassl, cultivars, cultivar-derived mutants and interspecific hybrids between S. officinarum and S. spontaneum. Six fixed primers, designed from sucrose- and cold tolerance-related EST (expressed sequence tags) sequences, paired with three arbitrary primers, were used to characterize the germplasm. Both the cluster and principal coordinate (PCoA) analyses placed the Erianthus spp. and Miscanthus spp. genotypes distinctly from each other and from the Saccharum species, thus, supporting their taxonomic classification as separate genera. Genotypes of the low sucrose and cold tolerant species, S. spontaneum, formed one distinct group, while the rest of the Saccharum species formed one interrelated cluster with no distinct subgroups. Sequence analysis of TRAP bands derived from a S. spontaneum genotype revealed homology with known gene sequences from other grass species includingSorghum.ABLASTn search using the homologous sequences from Sorghum matched with the S. officinarum GenBank accession from which the fixed TRAP primer was designed. These results ratify TRAPas a potentially useful marker technique for genetic diversity studies in sugarcane.
TL;DR: Having known QTL in MARS is most beneficial for traits controlled by a moderately large number of QTL (e.g., 40), and it is speculated that a combination of approaches would be needed to exploit information on markers for QTL themselves, markers linked to QTL, and unknown QTL.
Abstract: Genomics and post-genomics sciences are expected to uncover most, if not all, of the quantitative trait loci (QTL) in plants. Prior knowledge of QTL locations can then be exploited in marker-assisted recurrent selection (MARS). Our objectives were to determine (i) whether prior knowledge of QTL locations is advantageous in MARS, and (ii) whether knowledge of the QTL themselves, as opposed to knowledge of markers linked to QTL, is advantageous in MARS. We simulated MARS in a maize (Zea mays L.) F 2 population. We found that when 10 QTL controlled the trait, the percentage of known QTL that maximized the response to MARS was P Max = 100%. In contrast, P Max was often less than 100% when 40 or 100 QTL controlled the trait and QTL effects were estimated with a population size (N = 100) typically used in MARS. This result implied it was advantageous to exploit only the QTL with large effects and ignore those with small effects, even if the locations of all QTL were known. For a trait controlled by 40 QTL, the response was up to 50% greater when P Max = 70% of the QTL were known through markers for the QTL themselves rather than through linked markers. We conclude that having known QTL in MARS is most beneficial for traits controlled by a moderately large number of QTL (e.g., 40). We speculate that a combination of approaches would be needed to exploit information on markers for QTL themselves, markers linked to QTL, and unknown QTL.
TL;DR: The results indicated that stratified sampling based on seven primary ecotypes may represent an optimal strategy for assembling a representative core collection of Chinese soybean.
Abstract: China is the center of origin of soybean [Glycine max (L) Merr] and is therefore expected to represent a primary source of germplasm for this crop Genetic diversity assessments among Chinese soybean accessions should provide useful information for local and international soybean researchers to more effectively utilize this material A sample of 129 accessions were selected to represent phenotypic variability for 14 agronomic and morphological traits in the Chinese soybean collection These accessions were analyzed with 60 mapped simple sequence repeats (SSRs) to determine the genetic diversity represented In total, 732 alleles were detected (122 alleles per locus) and the polymorphic information content (PIC) among accessions varied from 05 to 092 with a mean of 078 Pairwise coefficients of genetic distance among all accessions ranged from 005 to 091 (mean 023) Unweighted pair-group method arithmetic average (UPGMA) analysis showed that the accessions formed five major clusters; two contained primarily Northern ecotypes, one contained primarily Yellow River Valley ecotypes, and one contained Southern ecotypes The fifth cluster contained a mixture of Northern and Yellow River Valley ecotypes Accessions from the lower regions of the Yellow River Valley possessed the greatest allelic richness, had the lowest pairwise genetic diversity estimates, and were dispersed throughout the five clusters, suggesting that the Yellow River Valley may be center of diversity for Chinese cultivated soybean The results indicated that stratified sampling based on seven primary ecotypes may represent an optimal strategy for assembling a representative core collection of Chinese soybean
TL;DR: The objectives of this study were to fine map the QTL and to determine if additional recombination could reduce the inverse phenotypic relationship between seed protein concentration and yield and oil concentration and to definitively conclude whether the protein QTL controls these other traits through pleiotropy.
Abstract: Soybean [Glycine max (L.) Merr.j is primarily grown as a source of protein and oil. A quantitative trait locus (QTL) controlling seed protein concentration was previously mapped to linkage group (LG) I of soybean. The objectives of this study were to fine map the QTL and to determine if additional recombination could reduce the inverse phenotypic relationship between seed protein concentration and yield and oil concentration. The fine mapping was done with two sets of backcross populations that were tested in the field and with genetic markers. These populations were developed by the introgression of a high protein allele from the Glycine soja Sieb and Zucc. plant introduction (PI) 468916 into the genetic background of the breeding line A81-356022. The first set (Set 1) included three populations of backcross-four (BC 4 ) lines, and the second set (Set 2) included four populations of BC 5 lines. The populations segregated for different segments of the genomic region where the QTL maps. Tests of the two sets of populations resulted in the localization of the QTL for protein and oil to a 3-cM interval between the simple sequence repeat (SSR) marker Satt239 and the amplified fragment length polymorphism (AFLP) marker ACG9b. The results from the agronomic trait evaluations were inconsistent, making it difficult to definitively conclude whether the protein QTL controls these other traits through pleiotropy.
TL;DR: Results indicate that PPO and o-diphenols can be an effective treatment to prevent protein loss in ensiled forage crops.
Abstract: Many forages experience significant proteolytic losses when preserved by ensiling. Such losses in alfalfa (Medicago sativa L.) are especially high, with degradation of 44 to 87% of the forage protein to nonprotein N (NPN). In contrast, red clover {Trifolium pratense L.) has up to 90% less proteolysis during ensiling. Here we demonstrate that the combination of polyphenol oxidase (PPO) and o-diphenol PPO substrates, both abundantly present in red clover, is responsible for postharvest proteolytic inhibition in this forage crop. Proteolysis in red clover leaf extracts increased nearly fivefold when endogenous o-diphenols were removed by gel filtration but returned to starting levels by adding back an exogenous o-diphenol. Proteolysis in leaf extracts of red clover plants silenced for PPO expression was dramatically increased compared to control plants. Leaf extracts of transgenic alfalfa expressing a red clover PPO gene showed a nearly fivefold o-diphenol-dependent decrease in proteolysis compared to those of control alfalfa. We also demonstrate that PPO levels 10- to 20-fold lower than those typically found in red clover are sufficient for proteolytic inhibition, that as little as 0.25 μmol o-diphenol mg -1 protein has a substantial impact on proteolysis, that a wide variety of o-diphenols are functional substrates in proteolytic inhibition, and that proteolysis is reduced for PPO-expressing alfalfa in small-scale ensiling experiments. Together, these results indicate that PPO and o-diphenols can be an effective treatment to prevent protein loss in ensiled forage crops.
TL;DR: How these novel approaches to gene transfer can effectively supplement the conventional breeding programs is described, and the current resistance to acceptance of this novel technology should be assessed and overcome so that its full potential in crop improvement can be realized.
Abstract: The art of plant breeding was developed long before the laws of genetics became known. The advent of the principles of genetics at the turn of the last century catalyzed the growth of breeding, making it a science-based technology that has been instrumental in substantial improvements in crop plants. Largely through exploitation of hybrid vigor, grain yields of several cereal crops were substantially increased. Intervarietal and interspecific hybridizations, coupled with appropriate cytogenetic manipulations, proved useful in moving genes for resistance to diseases and insect pests from suitable alien donors into crop cultivars. Plant improvement has been further accelerated by biotechnological tools of gene transfer, to engineer new traits into plants that are very difficult to introduce by traditional breeding. The successful deployment of transgenic approaches to combat insect pests and diseases of important crops like rice (Oryza sativa L.), wheat (Triticum aestivum L.), maize (Zea mays L.), barley (Hordeum vulgare L.), and cotton (Gossypium hirsutum L.) is a remarkable accomplishment. Biofortification of crops constitutes another exciting development in tackling global hunger and malnutrition. Golden Rice, genetically enriched with vitamin A and iron, has, for example,the real potential of saving millions of lives. Yet another exciting application of transgenic technology is in the production of edible vaccines against deadly diseases. How these novel approaches to gene transfer can effectively supplement the conventional breeding programs is described. The current resistance to acceptance of this novel technology should be assessed and overcome so that its full potential in crop improvement can be realized. A PARAMOUNT FACTOR in the evolution of human civilizations was a steady supply of food. Food production is therefore the oldest profession of humanity. The processes of crop cultivation and selection were an integral part of human activity. Although early “plant breeding” was developed essentially as an art, its scientific basis became well established with the rediscovery of laws of genetics at the turn of the last century. And with the application of the principles of genetics to crop improvement, the period from 1930 to 1970 witnessed a phenomenal increase in crop yields, particularly of cereal grains (Khush, 1999). Largely through exploitation of hybrid vigor, maize, pearl millet [Pennisetum glaucum (L.) R. Br.], and sorghum [Sorghum bicolor (L.) Moench]registeredaconsiderableincreaseingrainyields
TL;DR: Results indicated that a single dominant gene controlled resistance in Jackson, a cultivar found to have strong antibiosis-type resistance to the soybean aphid, and there is no known genetic relationship between Jackson and Dowling.
Abstract: The soybean aphid, Aphis glycines Matsumura, has become established as a serious pest of soybean, Glycine max (L.) Merr., since it was first found in North America in 2000 and has caused millions of dollars in economic losses. While the application of chemical insecticides is the only means to control the soybean aphid at present, genetic resistance to the aphid was recently discovered in soybean. A single dominant gene named Rag1 that controls resistance to the soybean aphid was found in the cultivar Dowling. Another cultivar found to have strong antibiosis-type resistance to the soybean aphid was Jackson. The primary objective of this study was to determine the inheritance of resistance to the soybean aphid in Jackson. Segregation of resistance was analyzed in F2 and among F2–derived F3 (F2:3) families produced from crosses between Jackson and the susceptible soybean cultivar Loda. Segregation of F2 plants was 247 resistant to 97 susceptible and fit a 3:1 genetic ratio (P 5 0.17). Segregation among F2:3 families was not clear because a number of susceptible F2 plants did not produce a sufficient amount of seed for progeny testing. Ignoring the susceptible class, the segregation of F2:3 families fit a 1:2 (all resistant/segregating) ratio. These results indicated that a single dominant gene controlled resistance in Jackson. There is no known genetic relationship between Jackson and Dowling. The genetic relationship between Rag1 in Dowling and the gene in Jackson is unknown.
TL;DR: The results suggest that gene-based approaches can effectively use agricultural genomics data for cultivar performance prediction and may have multiple uses in plant breeding.
Abstract: Realizing the potential of agricultural genomics into practical applications requires quantitative predictions for complex traits and different genotypes and environmental conditions. The objective of this study was to develop and test a procedure for quantitative prediction of phenotypes as a function of environment and specific genetic loci in soybean [Glycine max (L.) Merrill]. We combined the ecophysiological model CROPGRO-Soybean with linear models that predict cultivar-specific parameters as functions of E loci. The procedure involved three steps: (i) a field experiment was conducted in Florida in 2001 to obtain phenotypic data for a set of near-isogenic lines (NILs) with known genotypes at six E loci; (ii) we used these data to estimate cultivar-specific parameters for CROPGRO-Soybean, minimizing root mean square error (RMSE) between observed and simulated values; (iii) these parameters were then expressed as linear functions of the (known) E loci. CROPGRO-Soybean predicted various phenological stages for the same NILs grown in 2002 in Florida with a RMSE of about 5 d using the E loci-derived parameters. A second evaluation of the approach used phenotypic data from cultivar trials conducted in Illinois. Cultivars were genotyped at the E loci using microsatellites. The model predicted time to maturity in the Illinois variety trials with RMSE around 7.5 d; it also explained 75% of the time-to-maturity variance and 54% of the yield variance. Our results suggest that gene-based approaches can effectively use agricultural genomics data for cultivar performance prediction. This technology may have multiple uses in plant breeding.
TL;DR: The successful hybridization between diploid spedes A. duranensis and A. hypogaea and the synthetic amphidiploid support the theory that these two diploids are the parents of the cultivated peanut.
Abstract: Genus Arachis L. includes 80 described species, of which 31 belong to section Arachis, including the two diploid spedes A. ipaensis Krapov. and W.C. Gregory and A. duranensis Krapov. and W.C. Gregory, considered the putative B and A genome parents of the cultivated peanut This work contributes to the study of evolution of the peanut (Arachis hypogaea L.), based on the successful hybridization between A. ipaensis and A. duranensis, chromosome doubling of the hybrid, and crosses between the synthetic amphidiploid and representatives of the diversity of the crop. Diploid hybrids between A. ipaensis and A. duranensis, confirmed by molecular markers, had pollen stains of 0.98%. Colchicine-induced tetraploids were confirmed by mitotic chromosome counts. Progeny from these amphidiploid plants had a 97.74% pollen stain and significant differences among structure sizes measured in diploid and tetraploid flowers. Hybrid individuals [A. hypogaea × (A. ipaensis x A. duranensis) 4x ] were produced from crosses involving all six botanical varieties of A. hypogaea. These hybrids indicate the evolutionary similarity between the wild species and the cultigen. The successful hybridization between diploid spedes A. ipaensis and A. duranensis and between A. hypogaea and the synthetic amphidiploid support the theory that these two diploids are the parents of the cultivated peanut. Resulting materials are of great importance to peanut breeding.