Geneticists and breeders are positioned to breed plants with root traits that improve productivity under drought. However, a better understanding of root functional traits and how traits are related to whole plant strategies to increase crop productivity under different drought conditions is needed. Root traits associated with maintaining plant productivity under drought include small fine root diameters, long specific root length, and considerable root length density, especially at depths in soil with available water. In environments with late season water deficits, small xylem diameters in targeted seminal roots save soil water deep in the soil profile for use during crop maturation and result in improved yields. Capacity for deep root growth and large xylem diameters in deep roots may also improve root acquisition of water when ample water at depth is available. Xylem pit anatomy that makes xylem less “leaky” and prone to cavitation warrants further exploration holding promise that such traits may improve plant productivity in water-limited environments without negatively impacting yield under adequate water conditions. Rapid resumption of root growth following soil rewetting may improve plant productivity under episodic drought. Genetic control of many of these traits through breeding appears feasible. Several recent reviews have covered methods for screening root traits but an appreciation for the complexity of root systems (e.g., functional differences between fine and coarse roots) needs to be paired with these methods to successfully identify relevant traits for crop improvement. Screening of root traits at early stages in plant development can proxy traits at mature stages but verification is needed on a case by case basis that traits are linked to increased crop productivity under drought. Examples in lesquerella (Physaria) and rice (Oryza) show approaches to phenotyping of root traits and current understanding of root trait genetics for breeding.

A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat association mapping panel. Genome-wide association mapping has become a widespread method of quantitative trait locus (QTL) identification for many crop plants including wheat (Triticum aestivum L.). Its benefit over traditional bi-parental mapping approaches depends on the extent of linkage disequilibrium in the mapping population. The objectives of this study were to determine linkage disequilibrium decay rate and population structure in a spring wheat association mapping panel (n = 285-294) and to identify markers associated with yield and yield components, morphological, phenological, and drought tolerance-related traits. The study was conducted under fully irrigated and rain-fed conditions at Greeley, CO, USA and Melkassa, Ethiopia in 2010 and 2011 (five total environments). Genotypic data were generated using diversity array technology markers. Linkage disequilibrium decay rate extended over a longer genetic distance for the D genome (6.8 cM) than for the A and B genomes (1.7 and 2.0 cM, respectively). Seven subpopulations were identified with population structure analysis. A stable QTL was detected for grain yield on chromosome 2DS both under irrigated and rain-fed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on chromosome 1BS co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on chromosome 1AL and 5A. After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield components and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs.

Interpretation of quantitative trait locus (QTL) studies of agronomic traits is limited by lack of knowledge of biochemical pathways leading to trait expression. To more fully elucidate the biological significance of detected QTL, we chose a trait that is the product of a well-characterized pathway, namely the concentration of maysin, a C-glycosyl flavone, in silks of maize, Zea mays L. Maysin is a host-plant resistance factor against the corn earworm, Helicoverpa zea (Boddie). We determined silk maysin concentrations and restriction fragment length polymorphism genotypes at flavonoid pathway loci or linked markers for 285 F2 plants derived from the cross of lines GT114 and GT119.Single-factor analysis of variance indicated that the p1 region on chromosome 1 accounted for 58.0%o of the phenotypic variance and showed additive gene action. The pi locus is a transcription activator for portions of the flavonoid pathway. A second QTL, represented by marker umclO5a near the brown pericarpi locus on chromosome 9, accounted for 10.8% of the variance. Gene action of this region was dominant for low maysin, but was only expressed in the presence of a functional pi allele. The model explaining the greatest proportion of phenotypic variance (75.9%) included pi, umclOSa, umcl66b (chromosome 1), ri (chromosome 10), and two epistatic interaction terms, pi x umclO5a and pi x ri. Our results provide evidence that regulatory loci have a central role and that there is a complex interplay among different branches of the flavonoid pathway in the expression of this trait.Development of molecular-marker linkage maps in many species facilitates the identification of chromosome regions associated with variation in quantitative traits (1). By dissecting the continuous phenotypic variation typical of many traits into contributions from discrete genetic factors, quantitative trait locus (QTL) studies provide insights into trait inheritance and genome organization, and often are sufficient to initiate marker-assisted selection. However, the biological interpretation of QTL data is generally limited by lack of knowledge of the genetics, biochemistry, and physiology underlying trait expression. To advance the level of QTL interpretation, we analyzed variation in an economically important trait that is determined by a well-characterized genetic and biochemical pathway.The corn earworm (CEW) is a major silk-and kernelfeeding insect pest of maize in the United States and parts of Latin America (2, 3). Host-plant resistance to CEW results from both antibiosis due to chemical factors in silks (stylar/ stigmatic tissue), and morphological features such as tight covering of the ear by husk leaves (4). Understanding of the nature of antibiosis to CEW was advanced when maysin (Fig. 1), a C-glycosyl flavone that inhibits CEW larval growth, was isolated from silks of the Mexican maize landrace "Zapalote Chico" (5). Later, Wiseman et al. (6) found a highly significant relationship between increased silk maysin concentration and reduced earworm ...

No abstract

The Rht-B1b and Rht-D1b alleles, which occur at homoeologous loci on chromosomes 4B and 4D, respec-Reduced height alleles at the Rht-B1 and Rht-D1 loci have been tively, reduce sensitivity to gibberellic acid (GA), which widely incorporated into wheat (Triticum aestivum L.) cultivars with the intent of improving partitioning of assimilates to grain. Although is necessary for stem elongation (Flintham et al., 1997). generally effective at increasing yield in high yield environments, In favorable environments, the reduced demand for astheir effects under heat and drought stress have been variable. We similates by a shorter stem results in improved assimilate undertook this study to evaluate the effects of the Rht-B1b and Rhtpartitioning to the developing head, leading to higher D1b dwarfing alleles in a recombinant inbred line (RIL) spring wheat spikelet fertility and more but smaller grain per head. population under a range of soil moisture conditions. Rht-B1 and Semidwarf wheats have smaller leaves, but compensate Rht-D1 genotypes of 140 RILs derived from a cross between 'Kauz' with increased photosynthetic rates resulting in a bioand MTRWA116 were determined by polymerase chain reactions mass similar to that of tall lines (LeCain et al., 1989;(PCR). The population was evaluated for yield and agronomic traits Morgan et al., 1990;Flintham et al., 1997). in four Colorado environments under fully irrigated, partially irri-The relative yield advantage of dwarf and semidwarf gated, and rainfed conditions in 2001 and 2002. Lines with both dwarfing alleles were significantly (P Ͻ 0.01) shorter, lower yielding, and cultivars varies with spring or winter habit, genetic backlater heading in all environments compared with lines with one or no ground, and environmental conditions. The benefits of dwarfing allele. Lines with both tall alleles performed equal to or the dwarfing alleles are more pronounced in high yieldbetter (P Ͻ 0.05) than all other classes for grain yield, test weight, ing winter wheat environments (Flintham et al., 1997) and kernel weight in all environments. Among lines with a single and in high yielding spring wheat locations at latitudes dwarfing allele, those with Rht-B1b on average outyielded those with less than 40Њ (Fischer and Quail, 1990). However, under Rht-D1b in the fully irrigated environment (5432 versus 4993 kg heat and drought stress, there may be no benefit of the ha Ϫ1 , P Ͻ 0.05), but elsewhere their yields did not differ (P Ͼ 0.05).dwarfing alleles in spring wheat (Flintham et al., 1997; Desirable values for most traits occurred across a relatively wide range Nizam Uddin and Marshall, 1989; Richards, 1992a,b). of plant heights, with the best performing lines either shorter lines inRichards (1992a) concluded that grain yield does not the tall class or taller lines in the semidwarf classes. edu).Published in Crop Sci. 45:939-947 (2005).

Plant breeders require genetic diversity to develop cultivars that are productive, nutritious, tolerant of biotic and abiotic stresses, and make efficient use of water and fertilizer. The USDA‐ARS National Plant Germplasm System (NPGS) is a major source for global plant genetic resources (PGR), with accessions representing improved cultivars, breeding lines, landraces, and crop wild relatives (CWR), coupled with passport and trait evaluation data. The goal of this article is to facilitate use of PGR in plant breeding programs. Our specific objectives are (i) to summarize the structure and operation of the NPGS and its consultative and support committees, (ii) to review current use of the system by plant breeders, (iii) to describe constraints to improving the utility of PGR, and (iv) to discuss ways in which the NPGS might evolve to better meet the challenges facing agriculture and society in coming decades. The NPGS will enhance its relevance to plant breeding provided there is (i) ongoing attention to filling the gaps in NPGS collections, especially for CWR; (ii) a major increase in efforts to phenotype and genotype accessions using standardized methods; (iii) enhanced information content of the Genetic Resources Information Network (GRIN)‐Global system and improved interoperability with other databases; (iv) increased attention to prebreeding activities; (v) improved training opportunities in practices for incorporating PGR in breeding programs; and (vi) expanded outreach efforts to strengthen public support for the NPGS. We believe these steps will be implemented most effectively through coordinated efforts among USDA‐ARS, universities, the private sector, and international partners.

Heading date in wheat (Triticum aestivum L.) and other small grain cereals is affected by the vernalization and photoperiod pathways. The reduced-height loci also have an effect on growth and development. Heading date, which occurs just prior to anthesis, was evaluated in a population of 299 hard winter wheat entries representative of the U.S. Great Plains region, grown in nine environments during 2011–2012 and 2012–2013. The germplasm was evaluated for candidate genes at vernalization (Vrn-A1, Vrn-B1, and Vrn-D1), photoperiod (Ppd-A1, Ppd-B1 and Ppd-D1), and reduced-height (Rht-B1 and Rht-D1) loci using polymerase chain reaction (PCR) and Kompetitive Allele Specific PCR (KASP) assays. Our objectives were to determine allelic variants known to affect flowering time, assess the effect of allelic variants on heading date, and investigate changes in the geographic and temporal distribution of alleles and haplotypes. Our analyses enhanced understanding of the roles developmental genes have on the timing of heading date in wheat under varying environmental conditions, which could be used by breeding programs to improve breeding strategies under current and future climate scenarios. The significant main effects and two-way interactions between the candidate genes explained an average of 44% of variability in heading date at each environment. Among the loci we evaluated, most of the variation in heading date was explained by Ppd-D1, Ppd-B1, and their interaction. The prevalence of the photoperiod sensitive alleles Ppd-A1b, Ppd-B1b, and Ppd-D1b has gradually decreased in U.S. Great Plains germplasm over the past century. There is also geographic variation for photoperiod sensitive and reduced-height alleles, with germplasm from breeding programs in the northern Great Plains having greater incidences of the photoperiod sensitive alleles and lower incidence of the semi-dwarf alleles than germplasm from breeding programs in the central or southern plains.

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl f lavone synthesized in silks via a branch of the well characterized f lavonoid pathway. Our results using f lavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for ''channeling'' of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting f lavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits.The past decade has seen an explosion of information on the structure, organization, and functions of the maize (Zea mays L.) genome, including the development of high density molecular marker maps. One application of new mapping technologies has been the genetic dissection of quantitative traits with much greater precision than was previously possible (1, 2). Still, the quantitative trait loci (QTLs) detected are generally rather poorly defined regions, and the size of a QTL's phenotypic effect is sometimes confounded with its location relative to the nearest marker or to a nearby QTL. For most traits, genetic and biochemical information on metabolic pathways is extremely limited, and, therefore, it is difficult to interpret QTL results in terms of regulatory and structural genes, duplicate function loci, feedback inhibition, branched pathways, or other phenomena affecting trait expression. Our goal in this research project is to analyze the genetic control of a quantitative trait of economic importance [antibiosis to the corn earworm (CEW)] and to interpret the results in terms of the well characterized flavonoid pathway.The CEW Helicoverpa zea (Boddie) is a major insect pest of maize and other crops (cotton, soybeans, peanuts) in the United States and elsewhere in the Western Hemisphere (3, 4). Corn earworm eggs are laid on the silks, and the larvae access the ear by feeding through the silk channel. Host-plant resistance to CEW by antibiosis is caused by the presence of the C-glycosyl flavones maysin, apimaysin, and methoxymaysin and related compounds (Fig.