An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.     

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. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population

The traits of elongation, volume expansion, and water absorption are very important in determining the quality of cooked rice grains. In this study, quantitative trait loci (QTL) analysis of these traits was performed using a recombinant inbred population derived from a cross between two indica cultivars, ‘Zhenshan 97’ and ‘Minghui 63 ,’ which are the parents of the most widely grown hybrid rice in China. Using a linkage map based on 221 molecular marker loci covering a total of 1796 cM, a total of 33 QTLs were identified for the nine traits tested. QTLs were detected on chromosomes 1– 3 , 5– 9 , and 11 , respectively. The QTLs identified included three for cooked rice grain length elongation (chromosomes 2 , 6 , and 11), six for width expansion (chromosomes 1‐ 3 , 6 , 9 , and 11) and two for water absorption (chromosomes 2 and 6). Interestingly, a single QTL located near the wx gene on chromosome 6 seemed to influence all the traits tested for the cooked rice quality.     

Development of an interspecific Vigna linkage map between Vigna umbellata (Thunb.) Ohwi & Ohashi and V. nakashimae (Ohwi) Ohwi & Ohashi and its use in analysis of bruchid resistance and comparative genomics

To facilitate transfer of bruchid resistance to azuki bean (Vigna angularis) from its relatives an interspecific mapping population was made between rice bean, V. umbellata, and the related wild species V. nakashimae. The V. umbellata parent is completely resistant and V. nakashimae is completely susceptible to the bruchid beetle pests, azuki bean weevil (Callosobruchus chinensis) and cowpea weevil (C. maculatus). There is very low cross compatibility between V. umbellata and azuki bean. Therefore, V. nakashimae, that crosses with both V. umbellata and V. angularis without the need for embryo rescue, is used as a bridging species. A genetic linkage map was constructed based on an interspecific F₂ mapping population between V. umbellata and V. nakashimae consisting of 74 plants. A total of 175 DNA marker loci (74 RFLPs and 101 SSRs) were mapped on to 11 linkage groups spanning a total length of 652 cM. Segregation distortion was observed but only three markers were not linked to any linkage group due to severe segregation distortion. This interspecific genome map was compared with the genome map of azuki bean. Of 121 common markers on the two maps, 114 (94.2%) were located on the same linkage groups in both maps. The marker order was highly conserved between the two genome maps. Fifty F₂ plants that produced sufficient seeds were used for quantitative trait locus (QTL) analysis and locating gene(s) for C. chinensis and C. maculatus resistance in V. umbellata. The resistance reaction of these F₂ plants differed between C. chinensis and C. maculatus. Both resistances were quantitatively inherited with no F₂ plants completely susceptible to C. chinensis or C. maculatus. One putative QTL for resistance to each of these bruchid species was located on different linkage groups. Other putative QTLs associated with resistance to both C. chinensis and C. maculatus were localized on the same linkage group 1. Linked markers associated with the bruchid‐resistant QTL will facilitate their transfer to azuki bean breeding lines.     

Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato

Although the Advanced Backcross strategy has proven very useful for QTL detection in tomato, it has been used mainly in identifying QTL for agronomic traits such as yield, color, etc. Tomato flavor is an important quality characteristic, yet it has been difficult to assess flavor or traits that affect it. In this study the AB-QTL strategy was applied to four advanced backcross populations to identify QTL for biochemical properties that may contribute to the flavor of processed tomatoes, such as sugars and organic acids. A total of 222 QTL were identified for 15 traits, including flavor as assessed by a taste panel. Correlations of certain biochemicals with flavor and possible methods of assessing and improving flavor are discussed. In particular, QTL with very significant effects associated with the ratio of sugars/glutamic acid, a trait highly correlated with improved flavor, have been identified as good targets for future work in improving the flavor of tomatoes. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular mapping and characterization of traits controlling fiber quality in cotton

Cotton (Gossypium spp) is the world's leading natural fiber crop. Genetic manipulation continues to play a key role in the improvement of fiber quality properties. By use of DNA-based molecular markers and a polymorphic mapping population derived from an inter specific cross between TM-1 (G. hirsutum) and 3-79 (G. barbadense), thirteen quantitative trait loci (QTLs) controlling fiber quality properties were identified in 3-79, an extra long staple (ELS) cotton. Four QTLs influenced bundle fiber strength, three influenced fiber length, and six influenced fiber fineness. These QTLs were located on different chromosomes or linkage groups and collectively explained 30% to 60%of the total phenotypic variance for each fiber quality property in the F₂ population. The effects and modes of action for the individual QTLs were characterized with 3-79 alleles in TM-1 genetic background. The results indicated more recessive than dominant, with much less additive effect in the gene mode. Transgressive segregation was observed for fiber fineness that could be beneficial to improvement of this trait. Molecular markers linked to fiber quality QTLs would be most effective in marker-assisted selection (MAS) of these recessive alleles in cotton breeding programs. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTL analysis of seed dormancy in rice (Oryza sativa L.)

Effective cumulative temperature (ECT) after heading would be a more reasonable parameter for seed sampling of pre-harvest sprouting/seed dormancy (SD) tests in segregating populations than the days after flowering. SD is an important agronomic trait associated with grain yielding, eating quality and seed quality. To identify genomic regions affecting SD at different grain-filling temperatures, and to further examine the association between SD and ECT during grain-filling, 127 double haploid (DH) lines derived from a cross between ZYQ8 (indica)/JX17 (japonica) by anther culture were analyzed. The quantitative trait loci (QTLs) and their digenic epistasis for SD were identified using a molecular linkage map of this population. A total of four putative QTLs for SD (qSD-3, qSD-5, 6 and 11) were detected on chromosomes 3, 5, 6 and 11, together explaining 41.4% of the phenotypic variation. Nine pairs of digenic epistatic loci were associated with SD on all but chromosome 9, and their contributions to phenotypic variation varied from 2.87%–8.73%. The SD QTL on chromosome 3 was identical to the QTLs found in other mapping populations with different genetic backgrounds, which could be a desirable candidate for gene cloning and marker-assisted selection in rice breeding.     

Identification of quantitative trait loci underlying milling quality of rice (Oryza sativa) grains

Milling quality of rice grains is important to both producers and consumers. In this study, quantitative trait loci (QTLs) controlling brown rice rate (BR), milled rice recovery (MR) and head rice recovery (HR) were analysed by composite interval mapping over 2 years using 98 backcross inbred lines (BILs). A total of 12 QTLs for the three traits were detected, of which five were for BR, four for MR and three for HR. The proportion of phenotypic variation explained by individual QTLs ranged from 7.5 to 19.9%, and additive effects contributed by a single QTL accounted for 0.46 to 2.34% of the variation. QTL‐by‐environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years. Three of five QTLs for BR and two of four QTLs for MR were detected in 2 years, and all three QTLs for HR were detected in 1 year only. BR was significantly correlated with MR, and all four QTLs of MR were located in the same regions as those of BR. This indicated that QTLs for highly correlated traits could often be detected in the same interval.     

Phylogenetic analysis of complete 5′ external transcribed spacers of the 18S ribosomal RNA genes of diploid Aegilops and related species (Triticeae, Poaceae)

PCR systems were designed to amplify the entire 5 external transcribed spacer (ETS) region of the 18S rRNA gene of all the diploid species of Aegilops and several other taxa closely related to domesticated wheat. Phylogenetic analysis was performed on the complete ETS sequences using the neighbor-joining, maximum parsimony, and maximum likelihood methods. Among the individual taxa studied, speciation in Secale is very recent. In the case of the A genome diploids, the results support the theory that the A genomes of wheat have experienced reticulate evolution owing to introgression. The B and G genomes of tetraploid domesticated wheats form a clade with Ae. speltoides in which the B genome diverged first and the G genome more recently. It was demonstrated that the complete ETS sequences of the Triticeae yield coherent phylogenetic information. The ETS is a useful tool for studying the phylogeny of closely related species.     

Could early gene flow have created similar allozyme-gene frequencies in cultivated and wild barley?

The possible role of early gene flow between wild and cultivated barley in their similar esterase gene frequencies was tested in a simulation study. The hypothetical population consisted of 99.9% wild forms possessing three alleles of an esterase gene and 0.01% domesticated forms possessing one of these esterase alleles. Various rates of inbreeding, selection coefficients against the wild form and shifting cultivation methods were tested for their effect on the establishment of the domesticated form and the esterase gene flow between the two barley types. Of these factors, inbreeding rates, in the range of 90–99%, had the smallest effect on the establishment of the domesticated form under primitive cultivation. Via gene flow, the esterase allelic frequency in the domesticated form could be similar to that of the wild form under 90% outcrossing in the domesticated form for 115–230 years, an unrealistic situation for barley which normally exhibits about 1% outcrossing. It seems, therefore, that the similar esterase allelic frequencies in wild and cultivated barley is only partly due to gene flow, and it is more plausibly accounted for by multiple domestications.