are homozygous and their genotypes can be reproduced by different research groups for repeated experiments Molecular markers provide a rapid approach to breeding for dein a variety of environments (Mather and Jinks, 1977). sired agronomic traits. To use them, it is necessary to determine the linkage between quantitative trait loci (QTLs) and such markers. The
Many agronomic traits of interest to plant breeders are quantitative. Recombinant inbred (RI) lines are particularly useful in genetic mapping studies of quantitative traits. A recombinant inbred population was derived from the Glycine max (L.) Merr. parents ‘Minsoy’ and ‘Noir 1’. This soybean population was used to investigate the genetic basis of several agronomic traits: days to flower (Rl), days to maturity (R8), reproductive period (RS‐R1), plant height, lodging score, height divided by lodging (the ability of tall plants to stand upright), seed protein content, seed oil content, seed size, yield, seed number, yield divided by height (the yield from short plants), leaf width, leaf length, and leaf area. In this RI population, transgressive segregation was observed for all of these traits. As expected, height and lodging were correlated, as were height and maturity; height and maturity with yield; and leaf length and width with leaf area. Height divided by lodging and yield divided by height showed little correlation with other traits, indicating that these traits measured new plant phenotypes. A genetic map was constructed for this population, with restriction fragment length polymorphism markers, simple sequence repeat markers and classical markers. Approximately 2000 cM of linkage was defined. The data were used to identify quantitative trait loci (QTLs) by linking quantitative phenotypes to qualitative genetic markers. for many traits, a few QTLs accounted for a large proportion of the variation observed. QTLs for most of the traits were associated with three linkage groups, often with the same genetic locus within the linkage group. At the level of resolution of the genetic map for this population, it was not possible to determine whether these QTLs have pleiotrophic effects or are clusters of separate, tightly linked genes. The data suggest that separation of QTLs for different traits (such as maturity or lodging and yield) may be difficult, but that this RI population will be useful in resolving questions concerning marker assisted selection of quantitative traits.
Quantitative trait loci (QTL) were mapped in segregating progeny from a cross between two soybean (Glycine max (L.) Merr.) cultivars: 'Minsoy' (PI 27.890) and 'Noir 1' (PI 290.136). The 15 traits analyzed included reproductive, morphological, and seed traits, seed yield and carbon isotope discrimination ratios ((13)C/(12)C). Genetic variation was detected for all of the traits, and transgressive segregation was a common phenomenon. One hundred and thirty-two linked genetic markers and 24 additional unlinked markers were used to locate QTL by interval mapping and one-way analysis of variance, respectively. Quantitative trait loci controlling 11 of the 15 traits studied were localized to intervals in 6 linkage groups. Quantitative trait loci for developmental and morphological traits (R1, R5, R8, plant height, canopy height, leaf area, etc.) tended to be clustered in three intervals, two of which were also associated with seed yield. Quantitative trait loci for seed oil were separated from all the other QTL. Major QTL for maturity and plant height were linked to RFLP markers R79 (31% variation) and G173 (53% variation). Quantitative trait loci associated with unlinked markers included possible loci for seed protein and weight. Linkage between QTL is discussed in relation to the heritability and genetic correlation of the traits.
A large recombinant inbred population of soybean has been characterized for 220 restriction fragmentlength polymorphism (RFLP) unlinked locus (which, by itself, is not associated with trait variation). This type of interaction is shown schematically in Fig. 1. In this example, a difference in height produced by different alleles at locus 1 is conditional upon the presence of a Noir 1 allele at locus 2. Only the RI lines with the Noir 1 allele at locus 2 will show differences in height produced by the first locus. To identify such pairs of loci, we chose as the first locus QTL that had been found to explain significant variation in a quantitative trait. We then scanned through unlinked second loci, dividing the population of RI lines into four genotypic classes by pairing each of the alleles at the first locus with each of the alleles at the second locus. These pairwise comparisons have identified second loci with substantial epistatic effects on plant height and on other traits such as seed yield. MATERIALS AND METHODSThe soybean RI population used here and the measurement of the traits have been described in detail (7). Briefly
Round soybean seeds are sought-after for food-type soybean. Also the genetic control of seed geometry is of scientific interest. The objectives of this study were to estimate heritability and map quantitative trait loci (QTLs) responsible for seed shape traits. Three densely mapped recombinant inbred populations each with 192 segregants were used, Minsoy x Archer, Minsoy x Noir1, and Noir1 x Archer. A two rep two location experiment was conducted in Los Andes, Chile, and East Lansing, MI, USA. Seed height (SH), width (SW), length (SL), and seed volume (SV) as width x height x length were measured to determine seed shape. Heritability was estimated by variance component analysis. A total of 19 significant QTLs (LOD >or= 3.7) in ten linkage groups (LG) were detected for all the traits. Only one QTL was stable across populations and environments and six were stable in at least two populations in both environments. The amount of phenotypic variation explained by a single QTL varied from 7.5% for SH, to 18.5% for SW and at least 30% of the genetic variation for the traits is controlled by four QTL or less. All traits were highly correlated with each other in all populations with values ranging from 0.5 to 0.9, except for SL and SW that were not significantly correlated or had a low correlation in all populations. Narrow sense heritabilities for all traits ranged from 0.42 to 0.88. We note that LG u9, u11, and u14 are hot points of the genome for QTLs for various traits. The number and genomic distribution of the QTLs confirms the complex genetic control of seed shape. Transgressive segregation was observed for all traits suggesting that careful selection of parents with similar phenotypes but different genotypes using molecular markers can result in desirable transgressive segregants.
Phytophthora root rot, caused by Phytophthora megasperma Drechs. f. sp. glycinea T. Kuan & D.C. Erwin, is one of the most serious diseases of soybean [Glycine max (L.) Merr.]. Six loci with alleles giving race‐specific resistance of soybean to phytophthora have been reported. The first objective of this study was to map the phytophthora resistance (Rps) loci using restriction fragment length polymorphism (RFLP) markers. The second objective was to map the Rj2 locus for ineffective nodulation with RFLP markers, because of the linkage of Rj2 to Rps2. The mapping was conducted using a series of ‘Williams’ near‐isogenic lines (NILs) with each having one or two phytophthora resistance alleles. The NILs were screened with 141 mapped RFLP markers. At least one polymorphism was found between each NIL and the recurrent parent. Linkage tests among the polymorphic RFLP markers, Rps loci, and the RJ2 locus were conducted using F2 populations. Linkage was found between RFLP markers and Rpsl, Kps2, Rps3, Rps4, Rps5, and RJ2. Linkage was also found between Rps2 and Rj2.
Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1–LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.
In order to breed efficiently, it is necessary to identify individual quantitative trait loci (QTLs) as well as interactions between these loci and to determine which QTLs produce phenotypes that are environment specific. This can be done by linking QTLs to molecular markers. The objective of this research was to carry out such an analysis for yield, one of the most complex agronomic traits. To do this, recombinant inbred lines of soybean [Glycine max (L.) Merrill] were characterized for molecular genetic markers and analyzed for yield in different environments. Interactions between QTLs were identified by subdividing the segregants into four sub‐populations defined by molecular alleles at pairs of unlinked loci. Differences in the mean yields of these sub‐populations defined interactions between QTLs. Measurements of yield in genotyped, recombinant inbred populations derived from crosses of ‘Minsoy’ with ‘Archer’ (MA population) and ‘Noir 1’ with Archer (NA population) have identified a pair of interacting yield QTLs whose effect was independent of environment as well as a pair of loci whose interaction was environment specific. Each example of epistasis, involved an allele specific interaction between the two QTLs. In the NA population, a pair of QTLs was identified in which Noir 1 alleles interact to specify a significant increase in yield that is not environment specific. These loci, located on linkage groups (LG) U3 and U9, do not affect either height or maturity. In all environments, the interaction between the QTLs was significant. In the MA population, a pair of QTLs was identified in which the Minsoy alleles interact to specify a significant increase in yield. However, this significant interaction is environment specific. One of the loci (on LG U14) is also associated with effects on height, seed weight, and maturity that are found in other environments, but these latter effects do not appear to involve any interactions with other loci. The data from the MA population support the concept that interactions between QTLs also can result in location‐specific effects on quantitative traits.
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