Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments

Powdery mildew, caused by the ascomycete fungus Podosphaera leucotricha, is one of the most damaging diseases of apple worldwide. Polygenically determined resistance might contribute to a significant increase of resistance to this disease in new cultivars. A quantitative trait locus (QTL) analysis was performed in an F₁ progeny derived from a cross between the apple cultivar Discovery and the apple hybrid TN10-8. Powdery mildew incidence was assessed during four years (five seasons) in spring and/or autumn in a French local orchard. Seven additive and/or dominant QTLs were detected over the five seasons, with effects (R ²) ranging from 7.5% to 27.4% of the progeny phenotypic variation. Two QTLs, on linkage groups (LGs) 2 and 13, were consistently identified and accounted together from 29% to 37% of the phenotypic variation according to the year of assessment. The other QTLs were identified during one (LGs 1, 14), two (LG10), or three (LGs 8, 17) seasons. Their instability indicated a changing genetic determinism according to the year of assessment, for which several hypotheses may be put forward. The QTLs on LGs 2 and 8 mapped close to clusters of resistance gene analogs (RGAs) and major genes for resistance to mildew or apple scab previously identified. The stable QTLs identified on LGs 2 and 13, together with the strong effect QTL located on LG 8, are of special interest for breeding purposes, especially if combined with other major resistance genes.     

A multiparent advanced generation inter-cross population for genetic analysis in wheat

We present the first results from a novel multiparent advanced generation inter-cross (MAGIC) population derived from four elite wheat cultivars. The large size of this MAGIC population (1579 progeny), its diverse genetic composition and high levels of recombination all contribute to its value as a genetic resource. Applications of this resource include interrogation of the wheat genome and the analysis of gene-trait association in agronomically important wheat phenotypes. Here, we report the utilization of a MAGIC population for the first time for linkage map construction. We have constructed a linkage map with 1162 DArT, single nucleotide polymorphism and simple sequence repeat markers distributed across all 21 chromosomes. We benchmark this map against a high-density DArT consensus map created by integrating more than 100 biparental populations. The linkage map forms the basis for further exploration of the genetic architecture within the population, including characterization of linkage disequilibrium, founder contribution and inclusion of an alien introgression into the genetic map. Finally, we demonstrate the application of the resource for quantitative trait loci mapping using the complex traits plant height and hectolitre weight as a proof of principle.     

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     

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBD_L), among individuals without pedigree, given information on surrounding markers and population history. These IBD_L probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD_L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.     

水稻穗颈维管束及穗部性状的QTL分析

以籼稻 (OryzasativaL .ssp .indicaZYQ8)和粳稻 (O .sativassp .japonicaJX17)的杂交F1代花培加倍的DH群体为材料考察了该群体的穗颈节大小维管束数、一次枝梗数、每穗颖花数、穗颈节顶部直径和穗长 ,并用该群体构建的分子图谱进行数量性状座位 (QTL)分析。检测到控制大维管束的 3个QTL (qLVB_1、qLVB_6和qLVB_7)分别位于第 1、第 6和第 7染色体 ;控制小维管束的 2个QTL (qSVB_4和qSVB_6 )分别位于第 4和第 6染色体 ;控制一次枝梗的 4个QTL (qPRB_4a、qPRB_4b、qPRB_6和qPRB_7)分别位于第 4(2个 )、第 6和第 7染色体 ;每穗颖花数的 3个QTL (qSPN_4a、qSPN_4b和qSPN_6 )分别位于第 4(2个 )和第 6染色体上 ;穗颈节顶部直径的 5个QTL (qPTD_2、qPTD_5、qPTD_6、qPTD_8和qPTD_12 )分别位于第 2、第 5、第 6、第 8和第 12染色体 ;穗长的 3个QTL (qPL_4、qPL_6和qPL_8)分别位于第 4、第 6、第 8染色体上。其中qLVB_6、qSVB_6、qSPN_6、qPTD_6和qPL_6均位于第 6染色体的G12 2_G1314b之间 ;qPL_8和qPTD_8位于第 8染色体的GA40 8_BP12 7a之间 ;qPRB_4a和qSPN_4a位于第 4染色体的G177_CT2 0 6之间 ;qPL_4和qSPN_4b位于第 4染色体CT40 4_CT5 0 0之间 ;qSVB_4所在的区间与qPL_4、qSPN_4b和qPRB_4b所在的区间相邻。     

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.     

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R² at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea.     

The use marker alleles for the introgression of linked quantitative alleles

Summary It is shown that when an exotic strain and a commercial strain differ genetically at a quantitative locus and at an adjoining marker locus, repeated backcrosses to the commercial strain, retaining only backcross progeny carrying the exotic marker allele, will allow the effective introgression of the linked quantitative allele from the exotic to the commercial strain. The introgression procedure will be particularly effective when exotic and commercial strains differ at two nearby marker loci with the quantitative locus bracketed between them. The simultaneous introgression of a number of quantitative alleles from different exotic strains, and appropriate selection procedures in the intercross generations that follow are also considered.     

Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible “supergene” regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.     

Genetics of gene expression characterizes response to selective breeding for alcohol preference

Numerous selective breeding experiments have been performed with rodents, in an attempt to understand the genetic basis for innate differences in preference for alcohol consumption. Quantitative trait locus (QTL) analysis has been used to determine regions of the genome that are associated with the behavioral difference in alcohol preference/consumption. Recent work suggests that differences in gene expression represent a major genetic basis for complex traits. Therefore, the QTLs are likely to harbor regulatory regions (eQTLs) for the differentially expressed genes that are associated with the trait. In this study, we examined brain gene expression differences over generations of selection of the third replicate lines of high and low alcohol‐preferring (HAP3 and LAP3) mice, and determined regions of the genome that control the expression of these differentially expressed genes (_deeQTLs). We also determined eQTL regions (_rveQTLs) for genes that showed a decrease in variance of expression levels over the course of selection. We postulated that _deeQTLs that overlap with _rveQTLs, and also with phenotypic QTLs, represent genomic regions that are affected by the process of selection. These overlapping regions controlled the expression of candidate genes (that displayed differential expression and reduced variance of expression) for the predisposition to differences in alcohol consumption by the HAP3/LAP3 mice.