Here characterization of the root system in a set of wheat hybrids is used to identify some associations between individual traits and associate relevant loci with DNA sequence-based markers. Additionally, the relationship of shoot and root traits is considered to help draw some conclusions for future research to focus upon.The research plan is based on two hypotheses: first, a narrow seminal root angle in wheat is important for adaptation to drought by allowing deeper rooting and better water acquisition, and second, the relationship of root to shoot biomass will determine the overall performance of wheat under stressed conditions. It is proposed to concentrate on these traits because they are major keys to root distribution in the soil as well as growth dynamics of seminal roots. To accomplish this project, a set of doubled haploid mapping populations has been created and will be implemented. The primary goal in developing mapping populations is to identify loci that affect the expression of a trait within that population. Estimation of the magnitude of the genetic effect is also essential to these types of studies. In 1998 Beavis demonstrated that in populations numbering 100 progeny, the quantitative trait locus effects were greatly overestimated, in populations with 500 progeny the QTL effects were slightly overestimated while populations with 1000 individuals produced estimates close to the actual magnitude of QTL effects. That study highlighted the necessity for larger populations and the need for verification of QTL across populations. In another study by Stange et al. , high density genotyping was shown to improve QTL localization, effect estimates,growing strawberries hydroponically and resolve closely linked QTL. Three spring wheats, Foisy, Sonora, and Chiddam Blanc de Mars , with significant differences in root architecture, seminal root characteristics, and root biomass were used to create three mapping populations.

Crosses were made in such a way that each parent is present in two of the three populations: Sonora x CBdeM , Foisy x Sonora , CBdeM x Foisy . For each population ca. 150 lines were genotyped giving an effective population size of 300 lines for each parent. This crossing scheme provides for instant verification of QTLs across populations and narrowing in on the gene responsible for traits of interest. It is expected that reliable QTLs will be identified in at least two of three populations provided that parents are heterogeneous for the alleles. High density genotyping of these three populations was completed using the Illumina iSelect 90K SNP assay. SNP calls were made using the Polyploid Clustering Module of Genome Studio and linkage maps were created using JoinMap4 . Phenotyping for basic morphological traits such as plant height, awns and such physiological traits as flowering time, grain yield, etc., will permit associations with specific genomic regions and this in turn will verify map quality and provide general reference. These populations along with the linkage maps are publically available. Recently, QTL analysis for root traits has gained an increasing interest. Previously most research has been focused in rice and maize. Weaver was one of the first to detail various root morphology of different crops and look at distribution of roots in the soil. Root architecture is determined by growth angle, total root length, and lateral branching. In 1993, Oyanagi et al. hybridized a cultivar of wheat with a wide angle and one with a narrow angle. The F1 hybrid showed an angle equivalent to that of the parent with the wide angle, and the distribution among the F2 was bimodal, with most plants having wide values and a small group giving narrow values. Thus, it was assumed that wide root angle was controlled by a single gene.

Drawing ideas from maize research, Oyanagi suggested that gravitropic responses of roots would be the easiest to use for estimations of wheat root distribution in the soil. So far, no gene for this character has been identified in wheat. However, a gene was identified and cloned in rice , which was shown to control the gravitropic response of roots . Previous QTL analyses for seminal root angle have been conducted on different wheat populations . Both studies used a limited number of markers, SSR and DArT, respectively, and dealt with single populations. The population used by Hamada et al. consisted of F1 derived doubled haploids and the population of Christopher et al. consisted of F1 derived doubled haploids and BC1 derived doubled haploids. No QTL for root angles were detected by Hamada et al., nor were other QTLs for other root traits similar across both studies. A potential problem could be a lack of large phenotypic difference between the parents used; Christopher et al. report that one parent had a root angle of 39.6 degrees and the other had an angle of 41.3 degrees. As noted by Tanksley , the greater the phenotypic difference between two individuals used in deriving a segregating population the greater the chances are of detecting significant QTL. Hamada et al. did not report the average angle of either parent used to derive their mapping population. These examples show the need for verification of possible QTLs and further analysis with larger populations and a higher density of markers. Many root morphological traits are regulated by a number of small-effect loci that interact with the environment. This becomes very apparent when conducting experiments testing root biomass and length. In fact, in many cases the amount of plasticity due to the environment creates such large errors that it is often difficult to measure such traits accurately. For these reasons, Dorlodot et al. , suggested that process-based traits such as growth rate, branching frequency and tropism should be studied as opposed to „static traits‟ such as length, mass, and volume.

That being said, biomass can be an important factor, along with other root characters, that allows for improved drought tolerance. Larger root systems and deeper roots in the soil profile is an obvious strategy used by plants to acquire available water when rainfall is limited. As water becomes less available at the surface, crops not adapted to reach the water available lower in the soil profile suffer. It has been suggested that roots targeting water acquisition deep in the soil profile may be especially important for smaller statured plants such as rice, wheat,rolling bench and common bean . For these reasons efforts need to be made to develop cultivars better adapted to limited water, however, understanding the relationship between shoot and roots will be essential for any progress. Although plants with larger and deeper root systems may be able to explore more of the soil profile excessive allocation of resources to root growth may have a negative impact upon grain yields when water is more accessible or when compared to a lean root system that reaches deeper into the soil profile. Recently Lynch proposed an ideotype for maize roots that would optimize water and nitrogen acquisition, which may be relevant to other cereal root systems. This ideotype includes narrow seminal root angles with abundant lateral branching while maintaining an overall lean root system. The idea is that the root system cannot cost the plant too much when it is already under stressful conditions. Maintaining a large and costly root system could put strains on carbon and resource allocation causing reductions is yield. Not only will it be important to understand the relationship of roots and shoots but identifying loci controlling the two will help to understand the issues at hand as well. The only example in wheat, as far as I know of, QTL mapping for root biomass was done by Sharma et al., 2011. They mapped QTLs for different root traits, including that for root biomass, on the short arm of rye chromosome 1R in bread wheat using 1RS-1BS recombinant lines. Another example of identifying chromosome regions influencing root biomass comes from Ehdaie and Waines . In this paper they identified genomic regions for responsible for various traits by using telosomic lines in bread wheat. Beyond these two studies there is still a need for verification and identification of genes controlling root biomass.Persistent predictions of climate change and increased drought has led to an increased interest in crop root systems.

Drought tolerance is a complex trait and most root system traits are heavily influenced by the environment. Root system traits are quantitatively controlled and their plasticity makes them difficult to study. This calls for tools such as specifically designed mapping populations. Here three integrated mapping populations of doubled haploids were developed with a built in system for verification of quantitative trait loci across genetic backgrounds. The three parents, Sonora, Foisy, and Chiddam Blanc de Mars, are “traditional cultivars” selected from land races each being hundreds of years old and could be considered land races themselves. They were chosen for their contrasting phenotypes including drought tolerance and root traits. The populations were genotyped using the 90K Illumina SNP array and high marker density genetic linkage maps were generated and verified by mapping some important agronomic traits. Two major QTLs for awn type were mapped to chromosomes 5A and 6B, five major QTLs responsible for flowering time were located on chromosomes 2D, 5A, 5B, and 5D, and two major QTLs for hybrid necrosis were mapped to chromosomes 2B and 5B. These exercises show that the quality of the linkage maps can be trusted. It has also been demonstrated that the design and relationships of these populations allow for instant verification of traits of interest when all three are used together in evaluations. This new resource is available to those interested in genetic dissection of root traits, and should become a valuable tool for many related studies.This is understandable given the relative ease of studying shoots and leaves versus roots. It is, however, well recognized that roots are vital to a plants livelihood and certainly are no less important than the above-ground parts. As agriculture is facing changes in climate patterns and increased incidence of drought, roots are gaining more attention. In recent years, more articles have been published with a focus on root systems in crops than there has ever been since Weaver‟s groundwork on the subject. Of the top three cereal crops grown worldwide, rice and maize have received most of the attention for root system genetics . More recently, wheat root system genetics has also seen an increase in attention with hopes of improving drought tolerance. This makes sense in that wheat makes up nearly 20% of the world‟s caloric intake each year . However, when compared to rice and even maize the wheat genome is much more complex and makes quantitative studies that much more challenging. Not only is drought tolerance a quantitative trait but most root system traits are highly plastic and also quantitatively inherited . These facts make studying root systems and their relationship to drought tolerance a fairly daunting task. To simplify the process it has been suggested that drought-tolerance traits should be dissected using genomic tools such as quantitative trait locus mapping and micro-arrays . It is likely that certain root system traits are critical to improving drought tolerance in wheat and thus should be studied in more detail . Current research on rice and maize has shown that indeed roots are important factors in reducing yield losses under water-limited conditions in the field . Given that the root system of wheat has only recently gained interest, only a limited number of mapping populations have been developed specifically for this purpose. All existing populations have the disadvantage of not offering any quick verification of quantitative trait loci in different genetic backgrounds. For these reasons three integrated mapping populations of doubled haploids in hexaploid bread wheat were developed. The way in which these populations were developed allows for the simultaneous testing of QTLs in different genetic backgrounds. This provides instant verification of QTLs across genetic backgrounds as well as environments when all populations are included in experimental trials. In 2009 and 2010 Waines et al. evaluated 17 spring wheat land races and modern cultivars for root biomass. Their results were used to select the appropriate parents for the three mapping populations.