Segregation of infectious pancreatic necrosis resistance QTL in the early life cycle of Atlantic Salmon (Salmo salar)

In a previous study, three significant quantitative trait loci (QTL) associated with resistance to Infectious Pancreatic Necrosis (IPN) disease were identified by analysing challenge data from one sub-population of Landcatch Atlantic salmon (Salmo salar) smolt. While these QTL were shown to affect the resistance in seawater, their effect in freshwater was unknown. This study investigates the effect of these QTL on IPN resistance in salmon fry in freshwater. Twenty families with intermediate levels of IPN mortality were analysed from a freshwater challenge trial undertaken on a different sup-population of LNS salmon to that studied previously. Only the QTL from linkage group 21 (LG21) appeared to have a significant and large effect on resistance in freshwater; the same QTL was found to have the largest effect in seawater in the previous study. Variance component analysis showed a high heritability for the QTL: 0.45 ± 0.07 on the liability scale and 0.25 ± 0.05 on the observed scale. In a family where both parents were segregating for the QTL, there was a 0% vs. 100% mortality in homozygous offspring for resistant and susceptible QTL alleles. The finding that the same QTL has major effect in both freshwater and seawater has important practical implications, as this will allow the improvement of resistance in both phases through marker assisted selection by targeting this QTL. Moreover, the segregation of the LG21 QTL in a different sub-population gives further evidence of its association with IPN-resistance.     

Detection of linkage between marker loci and loci affecting quantitative traits in crosses between segregating populations

Summary By making use of pedigree information and information on marker-genotypes of the parent and F-1 individuals crossed to form an F-2 population, it is possible to carry out a linkage analysis between marker loci and loci affecting quantitative traits in a cross between segregating parent populations that are at fixation for alternative alleles at the QTL, but share the same alleles at the marker loci. For two-allele systems, depending on marker allele frequencies in the parent populations, 2–4 times as many F-2 offspring will have to be raised and scored for markers and quantitative traits in order to provide power equivalent to that obtained in a cross between fully inbred lines. Major savings in number of F-2 offspring raised can be achieved by scoring each parent pair for a large number of markers in each chromosomal region and scoring F-1 and F-2 offspring only for those markers for which the parents were homozygous for alternative alleles. For multiple allele systems, particularly when dealing with hypervariable loci, only 10%–20% additional F-2 offspring will have to be raised and scored to provide power equivalent to that obtained in a cross between inbred lines. When a resource population contains novel favorable alleles at quantitative trait loci that are not present (or rare) in a commercial population, analyses of this sort will enable the loci of interest to be identified, mapped and manipulated effectively in breeding programs.Contribution no. 2124-E, 1987 series from The Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel     

Linkage between isozyme markers and a locus affecting seed size in Phaseolus vulgaris L.

Summary Backcross and F₂ progenies were produced between two bean genotypes, XR-235 and Calima, which differ in seed weight by a factor of two. The small-seeded XR-235 was used as the pistillate and recurrent parent. These genotypes showed polymorphisms at nine isozyme loci and at the phaseolin locus. Seed size parameters (weight, length, width, and thickness) were determined for each BC₁ and F₂ individual, i.e., for seeds harvested from XR-235 after pollination with F₁ and from the F₁ after selfing, respectively. A combination of starch gel electrophoresis and enzyme activity staining was used to determine the genotype of each BC₁ and F₂ individual at the segregating loci. SDS-PAGE and Coomassie blue staining were used to determine geno-type at the phaseolin locus. Tests for independent assortment using two-way contingency and maximum likelihood tables revealed three linkage pairs: Aco-1 — 20 cM — Dia-1; Adh-1 — 2 cM — Got-2; and Est-2 — 11 cM — Pha. Statistical comparisons were made between the means of genotype classes at each segregating locus for all seed size parameters. The results from two independently obtained BC₁s and the F₂ consistently indicated that the Adh-1-Got-2 segment was linked to a locus that affected seed size and overcame maternal control over seed size. This locus has been designated Ssz-1. This gene exhibited additive gene action and accounted for 30–50% of the seed size difference between the parents.Florida Agricultural Experiment Station, Journal Series No. R00696     

Identification of quantitative trait loci for plant height, lodging, and maturity in a soybean population segregating for growth habit

The use of molecular markers to identify quantitative trait loci (QTLs) has the potential to enhance the efficiency of trait selection in plant breeding. The purpose of the present study was to identify additional QTLs for plant height, lodging, and maturity in a soybean, Glycine max (L.) Merr., population segregating for growth habit. In this study, 153 restriction fragment length polymorphisms (RFLP) and one morphological marker (Dt1) were used to identify QTLs associated with plant height, lodging, and maturity in 111 F₂-derived lines from a cross of PI 97100 and Coker 237. The F₂-derived lines and two parents were grown at Athens, Ga., and Blackville, S.C., in 1994 and evaluated for phenotypic traits. The genetic linkage map of these 143 loci covered about 1600 cM and converged into 23 linkage groups. Eleven markers remained unlinked. Using interval-mapping analysis for linked markers and single-factor analysis of variance (ANOVA), loci were tested for association with phenotypic data taken at each location as well as mean values over the two locations. In the combined analysis over locations, the major locus associated with plant height was identified as Dt1 on linkage group (LG) L. The Dt1 locus was also associated with lodging. This locus explained 67.7% of the total variation for plant height, and 56.4% for lodging. In addition, two QTLs for plant height (K007 on LG H and A516b on LG N) and one QTL for lodging (cr517 on LG J) were identified. For maturity, two independent QTLs were identified in intervals between R051 and N100, and between B032 and CpTI, on LG K. These QTLs explained 31.2% and 26.2% of the total variation for maturity, respectively. The same QTLs were identified for all traits at each location. This consistency of QTLs may be related to a few QTLs with large effects conditioning plant height, lodging, and maturity in this population.     

Salt tolerance in Lycopersicon species. IV. Efficiency of marker-assisted selection for salt tolerance improvement

The usefulness of marker-assisted selection (MAS) to develop salt-tolerant breeding lines from a F₂ derived from L. esculentum x L. pimpinellifolium has been studied. Interval mapping methodology of quantitative trait locus (QTL) analysis was used to locate more precisely previously detected salt tolerance QTLs. A new QTL for total fruit weight under salinity (TW) near TG24 was detected. Most of the detected QTLs [3 for TW, 5 for fruit number, (FN) and 4 for fruit weight (FW)] had low R ² values, except the FW QTL in the TG180-TG48 interval, which explains 36.6% of the total variance. Dominant and overdominant effects were detected at the QTLs for TW, whereas gene effects at the QTLs for FJV and FW ranged from additive to partial dominance. Phenotypic selection of F₂ familes and marker-assisted selection of F₃ families were carried out. Yield under salinity decreased in the F₂ generation. F₃ means were similar to those of the F₁ as a consequence of phentoypic selection. The most important selection response for every trait was obtained from the F₃ to F₄ where MAS was applied. While F₃ variation was mainly due to the within-family component, in the F₄ the FN and FW between-family component was larger than the within-family one, indicating an efficient compartmentalization and fixation of QTLs into the F₄ families. Comparison of the yield of these families under control versus saline conditions showed that fruit weight is a key trait to success in tomato salt-tolerance improvement using wild Lycopersicon germplasm. The QTLs we have detected under salinity seem to be also working under control conditions, although the interaction family x treatment was significant for TW, thereby explaining the fact that the selected families responded differently to salinity.     

Molecular markers associated with seed weight in two soybean populations

Seed weight (SW) is a component of soybean, Glycine max (L.) Merr., seed yield, as well as an important trait for food-type soybeans. Two soybean populations, 120 F₄-derived lines of YoungxPI416937 (Pop1) and 111 F₂-derived lines of PI97100xCoker 237 (Pop2), were mapped with RFLP makers to identify quantitative trait loci (QTLs) conditioning SW across environments and populations. The genetic map of Pop1 consisted of 155 loci covering 973 cM, whereas Pop2 involved 153 loci and covered 1600 cM of map distance. For Pop1, the phenotypic data were collected from Plains, GA., Windblow, N.C., and Plymouth, N.C., in 1994. For Pop2, data were collected from Athens, GA., in 1994 and 1995, and Blackville, S.C., in 1995. Based on single-factor analysis of variance (ANOVA), seven and nine independent loci were associated with SW in Pop1 and Pop2, respectively. Together the loci explained 73% of the variability in SW in Pop1 and 74% in Pop2. Transgressive segregation occurred among the progeny in both populations. The marker loci associated with SW were highly consistent across environments and years. Two QTLs on linkage group (LG) F and K were located at similar genomic regions in both populations. The high consistency of QTLs across environments indicates that effective marker-assisted selection is feasible for soybean SW.     

Genetic analysis of agronomic traits in a cross between sugarcane (Saccharum officinarum L.) and its presumed progenitor (S. robustum Brandes & Jesw. ex Grassl)

Saccharum robustum Brandes & Jesw. ex Grassl has been suggested as the immediate progenitor species of cultivated sugarcane (S. officinarum L.) [4]. Chromosome pairing and assortment in these two species were previously studied by genetic analysis of single-dose DNA markers in parents in and 44 F₁ progeny of a cross between euploid, meiotically regular 2n=80S. officinarum LA Purple andS. robustum Mol 5829 [2]. This same population was subsequently clonally propagated and evaluated in replicated trials for quantitative traits important to sugarcane breeders. Numbers of stalks, tasseled stalks, and stalks with smut, and the average diameter of two stalks were determined one day prior to harvest. At harvest, plant material from each plot was weighed and evaluated for pol (sucrose content) and fiber percentages. Clones were significantly different (P<0.01) for all traits analyzed. Associations of 83 single-dose arbitrarily primed PCR genetic markers with quantitative trait loci (QTL) of recorded traits was determined by single-factor ANOVA, and multiple regression. QTL analysis revealed markers significantly (P<0.05) associated with the expression of each trait analyzed. Markers associated with QTL after multiple regression were tested for digenic linear × linear epistatic interactions. The various multilocus models explained between 23% and 58% of the total phenotypic variation and 32% and 76% of the genotypic variation for the various traits. Digenic interactions were uncommon. Implications for marker-assisted selection in sugarcane and sugarcane domestication are discussed.     

QTL analysis: a simple ‘marker-regression’ approach

A method to locate quantitative trait loci (QTL) on a chromosome and to estimate their additive and dominance effects is described. It applies to generations derived from an F₁ by selfing or backcrossing and to doubled haploid lines, given that marker genotype information (RFLP, RAPD, etc.) and quantitative trait data are available. The method involves regressing the additive difference between marker genotype means at a locus against a function of the recombination frequency between that locus and a putative QTL. A QTL is located, as by other regression methods, at that point where the residual mean square is minimised. The estimates of location and gene effects are consistent and as reliable as conventional flanking-marker methods. Further applications include the ability to test for the presence of two, or more, linked QTL and to compare different crosses for the presence of common QTL. Furthermore, the technique is straightforward and may be programmed using standard pc-based statistical software.     

QTL analysis of trichome-mediated insect resistance in potato

Genetic mapping of several components of a complex type of insect resistance has been undertaken as a means toward more efficient use of the valuable characteristics of a wild relative of potato. RFLP maps constructed on interspecific diploid progenies of Solanum tuberosum × S. berthaultii were used in conjunction with morphological, biochemical and biological phenotyping to identify quantitative trait loci (QTLs) contributing to trichome-mediated insect resistance. By superimposing QTL data for a wide range of phenotypes including biochemical assays, correlative and direct screens for insect resistance, and adaptation to the target environment on the genetic maps, we have addressed the organization, action and interaction of genes controlling the resistance mechanism. The outcome contributes to an understanding of the association between component traits and between desirable and undesirable features of the donor species generated in an applied breeding program. Research is proceeding toward the development of selectable markers for the introgression and transfer of this resistance among potato gene pools.     

Location of a gene regulating drought-induced abscisic acid production on the long arm of chromosome 5A of wheat

The accumulation of abscisic acid (ABA) by detached and partially dehydrated wheat leaves is known to be inherited in a quantitative manner. The location of genes having a major effect on drought-induced ABA accumulation in wheat was determined using a set of single chromosome substitution lines and populations derived from a cross between a high-ABA- and a low-ABA-producing genotype. Examination of a series of chromosome substitution lines of the high-ABA genotype Ciano 67 into the low-ABA recipient Chinese Spring showed that chromosome 5A carries gene(s) that have a major influence on ABA accumulation in a drought test with detached and partially dehydrated leaves (DLT). A similar DLT was used to examine ABA accumulation in a population of F₂ plants and doubled haploid (DH) lines derived from the cross between Chinese Spring (low-ABA) and SQ1 (high-ABA) in which the F₂ population (139 plants) and DH lines (96 lines) were also mapped partially with molecular markers. Analysis of variance of ABA accumulation between and within marker allele classes in the F₂ confirmed the location of a gene(s) regulating ABA accumulation on the long arm of chromosome 5A. MAPMAKERQTL showed the most likely position for the ABA quantitative trait locus (QTL) to be between the loci Xpsr575 and Xpsr426, about 8 cM from Xpsr426. A similar trend for high ABA accumulation was found in DH lines having the SQ1 allele at marker loci in the same region of chromosome 5AL, but the QTL effect was not significant. The function of the QTL is discussed.