Effectiveness Of Marker-assisted Selection Research Articles

Marker-assisted versus phenotypic selection for iron-deficiency chlorosis in soybean

Iron-deficiency chlorosis (IDC) is an important agronomic trait when soybean (Glycine max (L.) Merr.) is planted on calcareous soil. Breeders need confirmation that marker-QTL (quantitative trait loci) associations developed using association mapping, will be effective in a different set of genotypes than the ones used to identify those markers. Marker-QTL associations that had previously been identified in separate mapping experiments were evaluated. Marker-assisted selection (MAS) was compared to phenotypic selection (PS) to evaluate the association mapping approach to identifying markers. The PS or MAS criteria were used to select the 20 most IDC-tolerant and IDC-susceptible lines, based on three 2009 selection sites. Three sites in 2010 were used as validation to compare the effectiveness of the different selection criteria. A random sample (RS) was generated as a control. When validation was conducted averaged across three 2010 sites, PS was the best method to select for IDC with a mean of 1.78, compared to MAS with a mean of 2.05. Since PS was so effective the process of genotyping, which is required for MAS, was unnecessary. The additive effects of QTL that had been estimated from the original mapping experiments were biased upward when compared to QTL effects estimated from the 2009 data. Also, many markers in the target population of experimental lines did not have a gene frequency of 0.5, which greatly reduced the effectiveness of MAS.

Genetic mapping of a fusarium wilt resistance gene in Brassica oleracea

Fusarium wilt caused by Fusarium oxysporum f. sp. conglutinans is one of the most important diseases of Brassica crops, resulting in severe reductions in yield and quality. To characterize the inheritance pattern of fusarium resistance, a cross between a susceptible broccoli and a resistant cabbage was subjected to segregation analysis. Results indicated that resistance was controlled by a single dominant allele. This gene was named Foc-Bo1 and mapped to linkage group seven (O7) by both the segregation test and quantitative trait locus (QTL) analysis. The QTL on O7 was detected with a logarithm of odds score (LOD) of 19.5, which was above the threshold value with genome-wide 1% significance level (2.01). A minor QTL was also detected on O4 with a LOD score of 2.06. Inoculation tests indicated that stable expression of fusarium resistance at high temperatures required Foc-Bo1 homozygosity. The association between Foc-Bo1 and the closest simple sequence repeat marker (KBrS003O1N10) was analyzed in three F3 populations. Based on these studies, KBrS003O1N10 represents an effective marker-assisted selection (MAS) tool for breeding fusarium wilt resistance into Brassica oleracea crops. To our knowledge, this is the first paper to map the fusarium-resistance gene in Brassica species and to validate the effectiveness of MAS in improving fusarium resistance in these important plants.

Marker-assisted backcross selection in an interspecific Cucumis population broadens the genetic base of cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.) is a major cucurbit vegetable species whose genetic base has been drastically reduced during its domestication. The crop’s narrow genetic base (3–12% DNA polymorphism) has resulted from the use of limited genetic material and intense selection during plant improvement. Recently, however, interspecific hybridization has been successful in Cucumis via mating of C. hystrix Chakr. and C. sativus, which resulted in the amphidiploid C. hytivus. We report herein a marker-assisted strategy for increasing genetic diversity in cucumber through introgression backcrossing employing C. hytivus. The comparatively late-flowering but high-yielding, indeterminate, monoecious line WI 7012A (P1; donor parent) derived from a C. hytivus × C. sativus-derived line (long-fruited Chinese C. sativus cv. Beijingjietou) was initially crossed to the determinate, gynoecious C. sativus line WI 7023A (P2; recurrent parent 1), and then advanced backcross generation progeny (BC2) were crossed with the gynoecious indeterminate line WI 9-6A (P3; recurrent parent 2). More specifically, a single F1 individual (P1 × P2) was backcrossed to P2, and then BC progeny were crossed to P2 and P3, where marker-assisted selection (MAS) for genetic diversity (8 mapped and 16 unmapped markers; designated Sel) or no selection (designated NSel) was applied to produce BC3P2 (Sel) and BC3P3 (Sel), and BC2P2 (NSel) and BC2P2S1 (NSel) progeny. Relative vegetative growth, number of lateral branches (LB), days to flowering (DF), yield (fruit number), and fruit quality [as measured by length:diameter (L:D) and endocarp:total diameter (E:T) ratios] were assessed in parents and cross-progeny. DF varied from ~20 (BC3P2Sel) to ~25 days (BC2P3Sel) among the populations examined, where progeny derived from P2 possessed the shortest DF. Differences in cumulative yield among the populations over six harvests were detected, varying from ~8 fruits per plant in BC3P2 (Sel) to ~39 fruits per plant in BC2P3 (Sel). Although the vigorous vegetative growth of line P1 was observed in its backcross progeny, highly heterozygous and polymorphic backcross progeny derived from P3 were comparatively more vigorous and bore many high-quality fruit. Response to selection was detected for LB, DF, L:D, and E:T, but the effectiveness of MAS depended upon the parental lines used. Data indicate that the genetic diversity of commercial cucumber can be increased by introgression of the C. hystrix genome through backcrossing.

Comparative analysis of marker-assisted and phenotypic selection for yield components in cucumber

Theoretical studies suggest that marker-assisted selection (MAS) has case-specific advantages over phenotypic selection (PHE) for selection of quantitative traits. However, few studies have been conducted that empirically compare these selection methods in the context of a plant breeding program. For direct comparison of the effectiveness of MAS and PHE, four cucumber (Cucumis sativus L.; 2n = 2x = 14) inbred lines were intermated and then maternal bulks were used to create four base populations for recurrent mass selection. Each of these populations then underwent three cycles of PHE (open-field evaluations), MAS (genotyping at 18 marker loci), and random mating without selection. Both MAS and PHE were practiced for yield indirectly by selecting for four yield-component traits that are quantitatively inherited with 2-6 quantitative trait loci per trait. These traits were multiple lateral branching, gynoecious sex expression (gynoecy), earliness, and fruit length to diameter ratio. Both MAS and PHE were useful for multi-trait improvement, but their effectiveness depended upon the traits and populations under selection. Both MAS and PHE provided improvements in all traits under selection in at least one population, except for earliness, which did not respond to MAS. The populations with maternal parents that were inferior for a trait responded favorably to both MAS and PHE, while those with maternal parents of superior trait values either did not change or decreased during selection. Generally, PHE was most effective for gynoecy, earliness, and fruit length to diameter ratio, while MAS was most effective for multiple lateral branching and provided the only increase in yield (fruit per plant).

Marker-assisted selection for white mold resistance in common bean

A marker-assisted selection (MAS) study was conducted on two recombinant inbred line (RIL) populations of common bean (Phaseolus vulgaris) to test the effectiveness of MAS for resistance to white mold (Sclerotinia sclerotiorum). Markers for quantitative trait loci (QTL) on linkage groups B2 and B7 that were previously associated with resistance and plant architectural avoidance traits in the resistant parent Bunsi were chosen. In the Bunsi/Midland population 10 RILs included in the MAS selected group developed significantly less disease than the control group based on two years of field evaluation under white mold pressure. Growth habit had no significant effect on disease severity or incidence. In the Bunsi/Raven RIL population, disease scores in the MAS selected group were significantly lower than scores in the control group over two years. Additional progress in enhancing resistance to white mold was detected when yield and plant architecture were included in the selection process. Lower disease scores among RILs were observed when comparisons were made to RILs selected using MAS alone. Yield is an important trait that should be considered when selecting for resistance to white mold. Finally the potential of Bunsi as a genetic donor of QTL for white mold resistance was confirmed in both populations studied. This study supported the effectiveness of MAS to enhance selection for a complexly inherited trait such as resistance to white mold in common bean.

Wheat breeding assisted by markers: CIMMYT’s experience

Significant progress has been made in the characterization of loci controlling traits of importance using molecular markers. A number of markers are currently available in wheat for genes of interest to the breeders. Markers can be used to better characterize parental material, thereby improving the efficiency and effectiveness of parental selection for crossing and to track genes in segregating progenies through the selection process. Although a number of breeding programs are using molecular markers at modest levels, the costs associated with marker assisted selection (MAS) are frequently cited as the main constraint to their wide-spread use by plant breeders. However, this is likely to change when user-friendly, high-throughput, automated marker technologies based on single nucleotide polymorphisms become available. These evolving technologies will increase the number of available markers, and will improve the efficiency, throughput, and cost effectiveness of MAS, thereby making it more attractive and affordable to many breeding programs. This article examines the extent to which molecular markers have been used at the International Maize and Wheat Improvement Center (CIMMYT) in applied wheat breeding and reviews the limited publicly available information on MAS from other wheat breeding programs. As markers are currently available for relatively few traits, we believe that MAS must be integrated with ongoing conventional breeding to maximize its impact. When used in tandem with phenotypic selection, MAS will improve response to selection for certain traits, thereby increasing rates of genetic progress.

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

Effectiveness of marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTLs depends on the extent of LD and how it declines with distance between markers and QTLs in a population. Marker-QTL LD can be predicted from LD between markers. Our previous work evaluated LD measures between multi-allelic markers as predictors of usable LD of multi-allelic markers with QTLs. Since single nucleotide polymorphisms (SNPs) are the current marker of choice for high-density genotyping and LD-mapping of QTLs, the objective of this study was to use LD between multi-allelic markers to predict LD among biallelic SNPs or between SNPs and QTLs. Observable LD between multi-allelic markers was evaluated using nine measures. These included two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy-Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. The standardized chi-square measure that best predicted usable LD between multi-allelic markers and QTLs, based on our previous work, overestimated usable SNP-SNP or SNP-QTL LD. Instead, three other measures were found to be good predictors of usable SNP-SNP or SNP-QTL LD when LD is generated by drift. Therefore, the LD measure between multi-allelic markers that is best for predicting usable LD in a population depends on the type of markers (i.e. multi-allelic or biallelic) that will eventually be used for QTL mapping or MAS.

Selection for Lodging Resistance in Early Generations of Field Pea by Molecular Markers

Lodging resistance is a key objective in pea breeding programs. Implementation of marker‐assisted selection (MAS) in early generations could significantly enhance the efficiency of the breeding process compared with conventional selection in the F3 or later generations. The objective of this research was to evaluate the effectiveness of MAS for lodging resistance using a combination of a coupling‐phase linked marker A001 and a repulsion‐phase linked marker A004 in F2 generation field pea (Pisum sativum L.). Eight F2 populations consisting of 680 plants were scored for the markers. A total of 402 F3 families derived from MAS and 187 F3 families from unselected populations were evaluated for lodging reaction under field conditions. The lowest lodging scores for each population were obtained from plants with the combination of A001 marker presence and A004 marker absence. A higher proportion of lodging resistant F3 families was obtained from this marker combination as compared with phenotypic selection in the F3 generation. MAS was less expensive than phenotypic selection in the field. Thus, A001 and A004 are useful for MAS for lodging resistance in early generation pea breeding populations.

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL

Effectiveness of marker-assisted selection (MAS) and quantitative trait loci (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTL depends on the extent of LD and how it declines with distance in a population. Because marker-QTL LD cannot be observed directly, the objective of this study was to evaluate alternative measures of observable LD between multi-allelic markers as predictors of usable LD of multi-allelic markers with presumed biallelic QTL. Observable LD between marker pairs was evaluated using eight existing measures and one new measure. These consisted of two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy-Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. In simulated populations with a range of LD generated by drift and a range of marker polymorphism, marker-marker LD measured by a standardized chi-square statistic (denoted chi(2')) was found to be the best predictor of useable marker-QTL LD for a group of multi-allelic markers. Estimates of the level and decline of marker-marker LD with distance obtained from chi(2') were linearly and highly correlated with usable LD of those markers with QTL across population structures and marker polymorphism. Corresponding relationships were poorer for the other marker-marker LD measures. Therefore, when LD is generated by drift, chi(2') is recommended to quantify the amount and extent of usable LD in a population for QTL mapping and MAS based on multi-allelic markers.

Marker-assisted Selection for Improved Emergence and Eating Quality in Sweet Corn

Marker-assisted selection is proposed to be more effective than phenotypic selection in improving complex traits with low heritability. This study was designed to test empirically the efficiency of marker-assisted selection (MAS) vs. phenotypic selection (PS) in enhancing economically important characters in sweet corn using composite populations consisting of selected F2:3 families from two populations. In previous studies in our laboratory, these segregating populations were developed and assayed for genes influencing sweet corn emergence and eating quality. The 214 F2:3 families in the first population (W678su1 × IL731ase1) were classified into three sub-populations according to segregation for the se1gene. Marker-assisted selection and phenotypic selection were applied on the two homozygous sugary1 and sugary enhancer1 sub-populations separately. The second population consisted of 117 F2:3 families from the cross of Ia453sh2 × IL451bsh2. The genotypic selection was based on the polymorphism of five RFLP markers linked to QTL associated with significant effects on emergence and eating quality in the F2:3 generation. Twenty percent of the families in each population with the highest and lowest genotypic scores and phenotypic performance values were selected to constitute the MAS and PS composites, respectively. Emergence was evaluated in four different environments in Illinois and Wisconsin, while eating quality traits were evaluated in Illinois only. Results for emergence, with relatively high h2, in two out of three populations indicated that marker-assisted selection was superior to phenotypic selection. The effectiveness of MAS on enhancing stand establishment and eating quality will be discussed.

Marker‐Assisted Selection to Improve Drought Resistance in Common Bean

Breeding for a quantitative trait like drought resistance would be facilitated by the development of a method of marker‐assisted selection (MAS) that is capable of identifying high performing genotypes in early generations. Two recombinant inbred populations were grown from 1990 to 1994 at eight locations in Michigan and Mexico under stress and nonstress conditions to identify random amplified polymorphic DNA (RAPD) markers associated with drought resistance in common bean (Phaseolus vulgaris L.) Six‐hundred random decamer primers were screened against the parents of the two populations, 50% of which were polymorphic. Seventy of these polymorphic primers were screened against each population. Using one‐way analysis of variance and multiple regression, four RAPD markers were identified in one population and five in another that were consistently and significantly associated with yield under stress, yield under nonstress, and/or geometric mean yield across a broad range of environments. To test the effectiveness of MAS for drought resistance, markers were used to select genotypes from either extreme. Yield data from three locations were examined to evaluate the effectiveness of these markerbased selections. Marker‐assisted selection in the Sierra/AC1028 population was found to be effective in Michigan under severe stress and ineffective in Mexico under moderate stress. The five RAPD markers used for MAS in the Sierra/Lef‐2RB population improved performance 11% under stress and 8% under nonstress, whereas conventional selection based on yield performance failed to increase performance. Response to conventional selection was three times greater in the Sierra/AC1028 population, supporting the conclusion that the effectiveness of MAS is inversely proportional to the heritability of the trait under examination.