The advantage of using these recombinant breakpoints in developing a genetic map is in their physical differences from one another. Here, we used two methods to map. Firstly, we used the recombinant breakpoints to develop a genetic map of the arm, and secondly, we used the map to classify the breakpoints. Each interval or genetic distance between two markers is represented by one or more recombinant breakpoints that most often include both reciprocal configurations of the chromosomes. This physical separation of the breakpoints further refines the genetic map to 0.7 cM level. This reciprocal nature of chromosomes with breakpoints in any given interval will permit allocation of identified genetic loci to very narrow physical segments of rye chromatin. This may be a useful tool in dissecting the genetic components of a particular gene of interest or an important agronomic trait present on 1RS. Testing a total of 16 SSR and eSSR markers yielded four polymorphic amplified products which were comparable to the previous studies . Rödor et al. found different band sizes for cultivar and synthetic wheat, though the differences were comparable. Only 1 out of 9 eSSR markers could be mapped on 1BS-1RS. This low success rate may be due to low polymorphism between wheat and rye 1S arms. Whether this indicates high conservation of genic regions across species we cannot tell at this point. Peng et al. showed amplification of 15 wheat eSSR markers in rye as well as barley. They detected polymorphism between wheat and barley but did not mention polymorphism between wheat and rye. A comparison of the current 1RS-1BS map with the SSR and eSSR maps of the 1B chromosome shows a good agreement in marker order, location,grow lights and relative positions in its distal part, regardless of the projection mode used.
A similar approach was used to generate a genetic map of ph1b-induced 2R-2B intergeneric recombinants, with a similar success , validating the wide-hybrid approach to mapping. The integration of physical and molecular markers in the present 1RS-1BS map also provided the alignment of recombinant breakpoints over each map interval. This information offers great potential to study agronomic traits affected by the introduction of alien 1RS chromatin into wheat. Our working hypothesis was if a 1B+ line shows some specific trait then this trait should be absent in its complimentary T- line, and vice-versa. To check the applicability of this concept, we looked at different root characters in wheat. Studies during the past few years showed an increased root biomass in wheat with the alien 1RS chromosome arm over standard spring wheat Pavon 76 and found a positive correlation of increased root biomass with grain yield . Recent studies in rice and maize have also correlated the QTLs for root traits with QTLs for yield under field conditions . A major limitation to study roots is the difficulty in making observations as the process is very laborious and time consuming. In the present study, we tested only three recombinant chromosomes with breakpoints selected to divide the recombining portion of the arm into three segments of roughly similar lengths. The experiments were conducted in three years at the same months of the year, in replicated trials, to determine the magnitude of the genotype × year interaction and the repeatability of results from the sand-tube technique. Significant variation was observed from year to year , with considerably higher means in the third year. This might have been due to relatively lower temperatures in the third year providing better conditions for vegetative growth. The significant genotype × year interaction observed for number of roots greater than 30cm was due to only one genotype, T-14, producing more roots only in year 2.
Otherwise, other genotypes showed similar trends for this character across the three years. The lack of significant genotype × year interaction for most of the root characters examined indicated high repeatability for these root traits. Quade analysis used on rank sums separated the five genotypes in two groups viz., Pavon 1RS.1BL, 1B+2 and 1B+38 containing distal rye chromatin with higher rooting ability and Pavon 76 and T-14 lacking the distal rye segment with lower rooting ability . Overall, the five genotypes examined showed relatively small variation for shoot characters but they differed in root characteristics including root biomass. Based on the results, we propose the presence of quantitative trait locus or loci for root traits in the distal 15% of the physical length of 1RS arm. In cereals, most of the gene rich regions for agronomic traits are concentrated in the distal ends of the chromosomes . Kim et al. conducted field studies for the agronomic performance of 1R from different sources of origin. They found 1RS increase the grain yield significantly, and interestingly, all the lines with 1RS did not show significant differences for shoot biomass. They did not look at the root traits which could have also been useful. In a similar study, Waines et al. compared 1RS from different sources to study root biomass in hexaploid as well as tetraploid wheats. The translocated hexaploid wheats with 1RSAmigo and 1RSKavkaz showed 9% and 31% increase in root biomass than Pavon 76, respectively. Similar results were reported for the durum wheat “Aconchi” versus Aconchi with the 1RS arm. These studies point towards the definite presence of gene for greater rooting ability on 1RS, and also the differential expression of alleles from different sources of 1RS in root traits. In a recent study on rice root anatomy, Uga et al. identified a QTL for metaxylem anatomy on the distal end of the long arm of chromosome 10. In another comparative study of rye DNA sequences with rice genome, the distal end of the long arm of chromosome 10 of rice was syntenic to 1RS .
Both these studies provide evidence to support the general applicability of our mapping method to locate the probable region on 1RS, carrying gene/QTL for root traits. Our present finding on root studies prepares a platform to find gene/QTL for root traits on 1RS. Future work will focus on use of a larger number of recombinant lines to narrow down the QTL region of 1RS responsible for increased root traits and find the molecular markers linked to these QTL. Ultimately, this would lead to our goal of physical mapping and then positional cloning of the root QTL. The root, the hidden half of a plant, is important for numerous functions including water and nutrient uptake that make it difficult to over look the root’s importance to plant productivity . It is an irony that this organ has inspired fewer plant scientists to work on it than the number who work on above-ground plant parts. The limited research effort in improvement of roots may be because of the difficulty in observing, measuring and manipulating them .Very likely, those resistances facilitated the selection and establishment of a spontaneous centric rye-wheat translocation 1RS.1BL in place of chromosome 1B of bread wheat . The translocation spread throughout the world even when these resistance genes were not important,led grow lights and eventually made it into hundreds of released cultivars . It was realized that the translocation increased grain yield even in the absence of pathogens , and eventually, the yield gain was attributed to a substantially increased root biomass . A larger root system increases uptake of water and nutrients from the soil . Cereal roots have two main classes, seminal roots and nodal roots . Seminal roots originate from the germinating embryonic hypocotyls, and nodal roots emerge from the coleoptile nodes at the base of the apical culm . Weaver compared the root systems of rye and bread wheat, and reported rye had longer seminal roots. The genetic control of root characteristics is poorly understood as the growth pattern changes greatly depending on the environment and almost always it is obscured from direct observation. Root traits are believed to be complex and controlled by many genes, each with a small genetic effect. Genetic loci controlling such traits are called quantitative trait loci . With the advent of molecular markers, it has become possible to estimate the genome location and size of QTL, including those for root characters. Research has recently been undertaken to map root QTL in rice , maize , common bean , and Arabidopsis . In wheat, many QTL have been identified for above ground traits of agronomic importance but no information on root genes or QTL has been reported. Disregarding root pathogens, the most recent wheat gene catalogue contains not a single reference to roots . Most quantitative traits are determined by many interacting loci with small genetic effects that are modified by environmental factors . Interaction of these alleles at different loci is called epistasis . Epistasis is now considered an important source of genetic variation with some components, especially Additive × Additive receiving more attention due to their heritable nature .
Efficient methods have been developed to map QTL with additive effects but mapping QTL with epistatic effects is still at the juvenile stage. There were efforts to detect epistasis using Bayesian models but they were unable to guarantee detection of all such effects. The Bayesian approach uses a given prior distribution and Markov chain Monte Carlo sampling to infer posterior distribution conditional on the data . Recently, Xu developed an empirical Bayes method that requires no MCMC samplings, yet still estimates the variance parameters for the priors of the regression coefficients. Simultaneous estimation of additive effects of all individual markers along with epistatic effects from all combination of marker pairs made this approach for estimation of significant epistatic effects where many may go undetected. Recent studies have shown the efficiency of chromosome specific mapping populations over traditional crosses in detecting a given effect with fewer progenies . The power of such a population, in a statistical sense, has been demonstrated in animal studies such as mice . In plants, stepped aligned recombinant inbred strains were generated in Arabidopsis, using chromosome substitution strains , but there is no detailed report until now on using such a mapping population for analysis ofcomplex traits. It is another irony that chromosome substitution lines have been incorporated in wheat breeding programs since the 1950s but it is only now that they are being appreciated for generating a chromosome specific mapping population to study quantitative traits. This paper presents a first ever attempt to characterize QTL effects for wheat root traits, using the E-BAYES method in combination with a chromosome specific mapping population. Here, we report the detection of additive and epistatic effects and also further dissection of gene interaction effects into inter-genomic and intra-genomic epistatic effects. The root study was done on a total of 29 recombinant lines, each having a different recombination breakpoint. These 29 lines were selected from a population of 68 1RS-1BS recombinants, as used to generate 1RS-1BS integrated map . This map consisted of a total of 20 markers in 15 intervals spanning 35-40% of the physical length of the chromosome arm, with average spacing of ca. 2.5cM. Assuming the total map length of 50 cM , the 68 1RS-1BS recombination breakpoints bring the average resolution of this map to 0.7cM. Plants were grown in PVC tubes, 80 cm long and 10 cm in diameter and regularly watered. After 45 days plants were harvested, roots were washed by the floatation technique and various characters were measured. The experiment involved 32 lines including Pavon 76, Pavon 1RS.1BL and Pavon Dt. 1BL as checks, grown in a glasshouse for four seasons in a randomized complete block design with four replications. The shoot characters measured were; the longest leaf length, maximum width of the longest leaf, leaf area, plant height, number of tillers per plant, dry shoot biomass, and the root characters were; number of roots greater than 30 cm, longest root length, total length of roots greater than 30 cm, shallow root weight , deep root weight , total root weight , and root biomass to shoot biomass ratio. The genotype of each marker was coded as +1 for the wheat allele and -1 for the rye allele.