Important QTL Research Articles

Construction and characterization of a BAC library of soybean

We have constructed a soybean (Glycine max (L.) Merrill) bacterial artificial chromosome (BAC) library from green leaf protoplasts of the cultivar, Misuzudaizu. The library contains 53,760 clones with an average insert size of 116 kb. About 2.9% chloroplast DNA origin was revealed by PCR and colony hybridization. Apart from 2.8% clones having no insert, this library represents 5.2 genome equivalents. With this genome coverage, the probability of having any DNA sequence represented in the library is higher than 99.5%. Three-dimensional pools of the BAC library in combination with the use of a high efficiency genome scanning (HEGS) electrophoresis facilitate rapid and efficient PCR-based screening. An average of five positive clones were identified after screening the BAC library with SSR and STS markers. BAC-end walking was performed for three SSR associated BACs. This library will provide a good resource for positional cloning of agronomically and biologically important QTL genes that Misuzudaizu possesses.

Marker-assisted selection for complex trait in common bean (Phaseolus vulgaris L.) using QTL-based index

A procedure was developed for marker-assisted selection of complex traits for common bean (Phaseolus vulgarisL.) using an index based on QTL-linked markers and ultrametric genetic distances between lines and a target parent. A comparison of the mean seed yields of the top five lines selected by different schemes demonstrated that the highest yielding group was selected on the basis of a combination of phenotypic performance and a high QTL-based index,followed by groups identified by a high QTL-based-index, conventional selection,and a low QTL-based-index. This study demonstrated a simple way to use information obtained from QTL studies to make selection decisions. The study also showed that the use of the QTL-based-index in conjunction with the ultrametric genetic distance to the target parent would enablea plant breeder to select lines that retain important QTL in a desirable genetic background. Therefore, this type of MAS would be expected to be superior to the phenotypic selection.

Genetic analysis of grain protein-content, grain yield and thousand-kernel weight in bread wheat.

Grain yield and grain protein content are two very important traits in bread wheat. They are controlled by genetic factors, but environmental conditions considerably affect their expression. The aim of this study was to determine the genetic basis of these two traits by analysis of a segregating population of 194 F(7) recombinant inbred lines derived from a cross between two wheat varieties, grown at six locations in France in 1999. A genetic map of 254 loci was constructed, covering about 75% of the bread wheat genome. QTLs were detected for grain protein-content (GPC), yield and thousand-kernel weight (TKW). 'Stable' QTLs (i.e. detected in at least four of the six locations) were identified for grain protein-content on chromosomes 2A, 3A, 4D and 7D, each explaining about 10% of the phenotypic variation of GPC. For yield, only one important QTL was found on chromosome 7D, explaining up to 15.7% of the phenotypic variation. For TKW, three QTLs were detected on chromosomes 2B, 5B and 7A for all environments. No negative relationships between QTLs for yield and GPC were observed. Factorial Regression on GxE interaction allowed determination of some genetic regions involved in the differential reaction of genotypes to specific climatic factors, such as mean temperature and the number of days with a maximum temperature above 25 degrees C during grain filling.

Development of PCR-based assays for allelic discrimination in maize by using the 5′-nuclease procedure

We describe the development of non-electrophoresis-based PCR assays for the allelic discrimination at two linked loci flanking an important QTL controlling days to pollen shed in maize. The assays are based on the fluorogenic 5′-nuclease procedure (TaqMan), which allows for the direct detection of the PCR product by the release of a fluorescent reporter dye as a result of DNA amplification. The assays were developed after sequencing the alleles at both loci, by designing suitable primers and probes based on single nucleotide or insertion/deletion polymorphisms. The TaqMan procedure allowed for a fast and highly reproducible analysis directly in the PCR vials. The lack of any fragment separation step allows for an almost complete automation of the process thus making this technique particularly valuable for the large-scale screening required for map-based cloning projects and for marker-assisted selection, particularly when the results are needed in a short time.

Genetic dissection of the source-sink relationship affecting fecundity and yield in rice (shape Oryza sativa L.)

The genetic basis underlying the relationship between the source leaves (the top two leaves) and the sink capacity in rice was investigated in a replicated trial of 2418 F2 derived F4 progeny from an inter-subspecific cross between cv. Lemont (japonica) and cv. Teqing (indica) and a complete linkage map with 115 well distributed RFLP markers. Path analysis indicated that 50% of the phenotypic variation in the primary sink capacity-grain weight per panicle was attributable to variation of the flag leaf area. Thirteen QTL and 30 pairs of epistatic loci were identified, which influence the length, width and area of the source leaves and the size of the primary sink (panicles) panicle length, floret density and floret number per panicle. Two QTL (QLl3b and QLw4) and 7 pairs of epistatic loci are largely responsible for the observed relationship between the source leaves and the sink capacity. The others appear to primarily influence the shape of the source leaves or panicle length/branching, and contribute little to the observed source-sink relationship and partially explain the yield component compensation. Our results suggest that important QTL affecting the source leaves can be manipulated through marker-assisted selection to increase sink capacity, which might result in improved yield potential in rice.

Regions of the Genome That Affect Grain and Malt Quality in a North American Two‐Row Barley Cross

Malting is an important end use of barley (Hordeum vulgare L.). The suitability of barley for malting depends on numerous quality characteristics, all of which are affected by genetic and environmental variation and many of which are inter‐related. Here, our objective was to use genome mapping to improve knowledge about the genetic basis for variation and covariation in grain and malt quality characteristics. Kernel plumpness, kernel weight, grain protein, fine‐grind extract, fine‐coarse difference, soluble protein, extract β‐glucan, extract viscosity, diastatic power, and a‐amylase activity were measured on grain produced in six field environments, from parents and doubledhaploid progeny of a two‐row barley cross, ‘Harrington’/‘TR306’. Quantitative trait loci and QTL × environment interactions were detected by means of 127 mapped markers and two methods of QTL analysis: simple interval mapping (SIM) and simplified composite interval mapping (sCIM). Each trait was affected by two to four primary QTL (those detected using both SIM and sCIM) and similar numbers of secondary QTL (those detected by only one of SIM or sCIM). Together, these QTL explained 21 to 67% of the phenotypic variance per trait. The numbers, effects, and relative positions of these QTL were in concordance with the quantitative trait distributions and with correlations among traits. All chromosomes, except chromosome 2, contained regions with at least one important QTL. Several genomic regions affected multiple traits. Most QTL interacted with environment, but many showed effects consistent enough that they might serve as targets for marker‐assisted selection. There was little similarity in the QTL positions detected here and those detected previously for the same traits in crosses representing other germplasm groups.

Quantitative Trait Loci Determining Resistance to Bacterial Wilt in Tomato Cultivar Hawaii7996

Several loci governing resistance to bacterial wilt, a disease caused by Ralstonia solanacearum, have been mapped in tomato (Lycopersicon esculentum). An F2 population derived from a cross between a highly resistant cultivar, Hawaii7996, and a very susceptible line of L. pimpinellifolium, WVa700, was used to develop a map of molecular markers. The parental lines were screened for polymorphism using 462 RFLP probes with 14 restriction enzymes. Genetic mapping revealed that the distribution of polymorphisms was very uneven. Nevertheless, the extensive screening permitted development of a map covering much of the genome. Nine independent resistance tests were done on cuttings from plants of this population in a controlled environment culture chamber. In addition to the most important QTL detected on chromosome 6, analyses of our data using either nonparametric or interval mapping tests suggest the presence of another QTL on chromosome 4 (2 QTL) and weaker putative QTL at other map positions. Together these loci, all derived from the resistant parent Hawaii7996, account for 30 to 56% of the phenotypic variation observed.

Congenic strains reveal effects of the epilepsy quantitative trait locus, El2, separate from other El loci.

Congenic mouse strains made by transferring epilepsy predisposing alleles El1, El2, and El3 from the EL/Suz strain to the ABP/Le recipient were tested for seizure frequency following gentle rhythmic stimulation. Mice homozygous for El2, but not El1 or El3, experienced seizures much more frequently than ABP controls, while respective El1 homozygotes and El2 heterozygotes had only a modest increase over ABP, and El3 homozygotes showed no increase. Association between marker genotypes and seizure frequency in small intra-strain crosses showed that the phenotypic effects of El2 map to the selected interval, and that segregation of El2 accounts for virtually all genetic effects. However, in separating El2 from other EL susceptibility alleles, the seizure frequency phenotype was weaker and less heritable than in crosses between parental strains. These results confirm El2 as an important QTL and show that it has significant phenotypic effects in the absence of other EL-derived alleles, including El1. In addition, the present localization of El2 on Chr 2 suggests several potential candidate genes for El2, including the beta subunit of phospholipase-C. The approach to dissecting complex traits by making congenic strains for individual QTL is discussed.