Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum

Molecular markers associated with fiber development traits have the potential to play a key role in understanding of cotton fiber development. Seventeen SSRs out of 304 markers tested from MGHES (EST-SSR), JESPR (genomic SSR), and TMB (BAC-derived SSR) collections showed significant linkage associations (using a Kurskal-Wallis non-parametric test) with lint percentage QTL in a set of recombinant inbred cotton lines (RILs) segregating for lint percentage. The permutation test of these potential markers associated with lint percentage QTL(s) determined that 12 SSR markers have stable estimates, exceeding empirically chosen threshold significance values at or above α = 0.01. Interval mapping demonstrated that 9 SSRs with stable critical LOD threshold values at α = 0.01 have significant QTL effect. Multiple QTL-mapping (MQM) revealed that at least, two highly significant fiber development QTLs exist around regions TMB0471 and MGHES–31 (explained about 23–59% of the phenotypic variation of lint percentage) and around markers MGHES–31 and TMB0366 (accounted for 5.4–12.5% phenotypic variation of lint percentage). These markers, in particular fiber-specific EST-SSRs, might be the possible ‘candidate’ loci contributing for fiber development in cotton. BAC-derived SSRs associated with fiber trait are the possible markers that are useful for the identification of physical genomic contigs that contain fiber development genes. Several lint percentage trait associated SSR markers have been located to chromosomes 12, 18, 23, and 26 using deletion analysis in aneuploid chromosome substitution lines. Outcomes of the work may prove useful in understanding and revealing the molecular basis of the fiber development, and the utilization of these markers for development of superior cotton cultivars through marker-assisted selection (MAS) programs. I. Y. Abdurakhmonov and S. Saha contributed equally to the work     

Genetic analysis of pre-harvest sprouting in a durum wheat cross

Pre-harvest sprouting of durum wheat (Triticum turgidum L. var durum) reduces commercial grade, although the actual effects on processing quality are controversial. Little is known about the genetics of the dormancy component of pre-harvest sprouting resistance in durum. We studied the segregation of dormancy in 98 recombinant inbred lines from a cross of a relatively non-dormant line, CI13102, with a moderately dormant line, Kyle. The lines and parents were grown in field tests over three years, 1996, 1997 and 1998. Spikes were collected at approximately 20% moisture and stored at −23 ∘C. Hand-threshed grain of the lines was germinated, and number of seeds germinated was counted each day. A germination resistance index was calculated to characterize dormancy. Dormancy appeared to be complexly inherited in this cross. Lines were observed that were significantly (P < 0.05) more dormant than the parents. The lines transgressive for dormancy expressed in different combinations of the three environments, indicating an environmental interaction. DNA of lines and parents was tested with simple sequence repeat primers and AFLPs that were used in quantitative trait loci (QTL) analysis of dormancy. Significant QTLs for dormancy were found, with the most notable being on chromosome 1A, where other QTLs for pre-harvest sprouting resistance have been reported in common wheat.     

Mixed models including environmental covariables for studying QTL by environment interaction

The study of the phenotypic responses of a set of genotypes in their dependence on the environment has always been an important area of research in plant breeding. Non-parallelism of those responses is called genotype by environment interaction (GEI). GEI especially affects plant breeding strategies, when the phenotypic superiority of genotypes changes in relation to the environment. The study of the genetic basis of GEI involves the modelling of quantitative trait locus (QTL) expression in its dependence on environmental factors. We present a modelling framework for studying the interaction between QTL and environment, using regression models in a mixed model context. We integrate regression models for QTL main effect expression with factorial regression models for genotype by environment interaction, and, in addition, take care to model adequately the residual genetic variation. Factorial regression models describe GEI as differential genotypic sensitivity to one or more environmental covariables. We show how factorial regression models can be generalized to make also QTL expression dependent on environmental covariables. As an illustrative example, we reanalyzed yield data from the North American Barley Genome Project. QTL by environment interaction for yield, as identified at the 2H chromosome could be described as QTL expression in relation to the magnitude of the temperature range during heading. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mapping genes for double podding and other morphological traits in chickpea

Seed traits are important considerations for improving yield and product quality of chickpea (Cicer arietinum L.). The purpose of this study was to construct an intraspecific genetic linkage map and determine map positions of genes that confer double podding and seed traits using a population of 76 F₁₀ derived recombinant inbred lines (RILs) from the cross of ‘ICCV-2’ (large seeds and single pods) × ‘JG-62’ (small seeds and double podded). We used 55 sequence-tagged microsatellite sites (STMS), 20 random amplified polymorphic DNAs (RAPDs), 3inter-simple sequence repeats (ISSR) and 2 phenotypic markers to develop a genetic map that comprised 14 linkage groups covering297.5 cM. The gene for double podding (s) was mapped to linkage group 6 and linked to Tr44 and Tr35 at a distance of7.8 cM and 11.5 cM, respectively. The major gene for pigmentation, C, was mapped to linkage group 8 and was loosely linked to Tr33 at a distance of 13.5 cM. Four QTLs for 100 seed weight (located on LG4 and LG9), seed number plant^-1 (LG4), days to 50% flower (LG3) were identified. This intraspecific map of cultivated chickpea is the first that includes genes for important morphological traits. Synteny relationships among STMS markers appeared to be conserved on six linkage groups when our map was compared to the interspecific map presented by Winter et al. (2000). This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular and physical mapping of genes affecting awning in wheat

Quantitative trait loci (QTL) for three traits related to awning (awn length at the base, the middle and the top of the ear) in wheat were mapped in a doubled‐haploid line (DH) population derived from the cross between the cultivars ‘Courtot’ (awned) and ‘Chinese Spring’ (awnless) and grown in Clermont‐Ferrand, France, under natural field conditions. A molecular marker linkage map of this cross that was previously constructed based on 187 DH lines and 550 markers was used for the QTL mapping. The genome was well covered (more than 95%) and a set of anchor loci regularly spaced (one marker every 20.8 cM) was chosen for marker regression analysis. For each trait, only two consistent QTL were identified with individual effects ranging from 8.5 to 45.9% of the total phenotypic variation. These two QTL cosegregated with the genes Hd on chromosome 4A and B2 on chromosome 6B, which are known to inhibit awning. The results were confirmed using ‘Chinese Spring’ deletion lines of these two chromosomes, which have awned spikes, while ‘Chinese Spring’ is usually awnless. No quantitative trait locus was detected on chromosome 5A where the B1 awn‐inhibitor gene is located, suggesting that both ‘Courtot’ and ‘Chinese Spring’ have the same allelic constitution at this locus. The occurrence of awned speltoid spikes on the deletion lines of this chromosome suggests that ‘Chinese Spring’ and ‘Courtot’ have the dominant B1 allele, indicating that B1 alone has insufficient effect to induce complete awn inhibition.     

Quantitative trait loci for grain yield and yield components in a cross between a six-rowed and a two-rowed barley

Summary The positions of quantitative trait loci (QTL) for yield and yield components were estimated using a 85-point linkage map and phenotype data from a F₁-derived doubled haploid (DH) population of barley. Yield and its components were recorded in two growing seasons. Highly significant QTL effects were found for all traits at several sites in the genome. A major portion of the QTL was found on chromosome 2. The effect of the alleles in locus v on thousand grain weight and kernels per ear explained 70–80% of the genetic variation in the traits. QTL × year interaction was found for grain yield. Several different QTL were found within the two-rowed DH lines compared to those found in the six-rowed DH lines. Epistasis between locus v and several loci for yield and yield components indicates that genes are expressed differently in the two ear types. This may explain the difficulties of selecting high yielding lines from crosses between two-rowed and six-rowed barley.Abbreviations DH doubled haploid - QTL quantitative trait locus/loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism - T. Prentice Tystofte Prentice - V. Gold Vogelsanger Gold     

水、旱稻根基粗和抗旱系数QTL的标记辅助选择及验证

利用水、旱稻杂交、回交所产生的4个分离群体对RIL群体定位到的抗旱相关的根基粗、抗旱系数2个QTL进行了选择验证。结果表明，根基粗、抗旱系数QTL的两侧标记在不同群体、不同的遗传背景中遗传稳定。在旱田种植条件下，YIBC1、JIBC1、JIF2 3个分离群体携带有根基粗QTL brt4.1两侧标记有利等位基因的个体与没有携带brt4.1两侧     

Molecular Marker-Assisted Dissection of Quantitative Trait Loci for seven Morphological Traits in Rice (Oryza Sativa L.)

Summary The genetic dissection of morphological traits can helpful to evaluate their potential values as markers for rice genetic improvement. In this study, a RI population derived from a cross from Zhenshan97 and IRAT109 was used to dissect the genetic bases of seven morphological traits such as leaf sheath color (LSC), grain apiculus color (GAC), grain hairiness density (GHD), grain awn length (GAL), ratio of leaf length to width (RLW), leaf erectness (LER) and natural leaf rolling status (NLR). Totally, 26 main-effect QTLs and 22 epistatic QTLs were detected. Of them, 11 main-effect and 3 epistatic QTLs expressed environmental interactions. GAC controlled by a single gene could be regarded as the most useful marker. LSC controlled by two major interacted main-effect QTLs, but with no environmental interaction, is suitable to become morphological marker. LSC will be a very efficient morphological marker for identification of hybrid plants at rice seedling stage when the two major QTLs are introduced into male sterile line and restorer line separately. GHD controlled by a major QTL and a few minor QTLs with comparative low QEIs could also be used as marker. The traits GAL, NLR, RLW and LER, which were controlled by a number of minor effect QTLs and affected by environmental conditions could not be used as marker. But the QTLs with large effects, such as nrl8, can be targeted for corresponding trait improvement through marker-aided selection in rice breeding.     

Mapping and validation of PCR-based markers associated with a major QTL for seed dormancy in wheat

Seed dormancy is one of the important factors controlling pre-harvest sprouting (PHS) resistance in wheat. We identified a major quantitative trait locus (QTL) for seed dormancy on the long arm of wheat chromosome 4A (4AL) via simple sequence repeat (SSR)-based genetic mapping using doubled haploid lines from a cross between Japanese PHS resistant variety ‘Kitamoe’ and the Alpine non-resistant variety “Münstertaler” (K/M). The QTL explained 43.3% of total phenotypic variation for seed dormancy under greenhouse conditions. SSR markers flanking the QTL were assigned to the chromosome long arm fraction length 0.59–0.66 on the basis of chromosome deletion analysis, suggesting that the gene(s) controlling seed dormancy are probably located within this region. Under greenhouse conditions, the QTL explained 28.5 and 39.0% of total phenotypic variation for seed dormancy in Haruyutaka/Leader (HT/L) and OS21-5/Haruyokoi (O/HK) populations, respectively. However, in field conditions, the effect was relatively low or not significant in both the K/M and HT/L populations. These markers were considered to be widely useful in common with various genetic backgrounds for improvement of seed dormancy through the use of marker-assisted selection. Further detailed research using near isogenic lines will be needed to define how this major QTL interacts with environmental conditions in our area.     

Development of synthetic Brassica napus lines for the analysis of “fixed heterosis” in allopolyploid plants

Summary Allopolyploids are widely spread in the plant kingdom. Their success might be explained by positive interactions between homoeologous genes on their different genomes, similar to the positive interactions between different alleles of one gene causing heterosis in heterozygous diploid genotypes. In allopolyploids, such interactions can also occur in homozygous genotypes, and may therefore be called “fixed heterosis”. As to our knowledge, no experimental data are available to support this hypothesis. We propose an experimental approach to quantify “fixed heterosis” in resynthesised Brassica napus and the detection of loci contributing to “fixed heterosis” via comparative QTL mapping in B. napus and its parental species B. rapa and B. oleracea. In order to develop a genetically balanced material, interspecific crosses between 21 Brassica rapa and 16 Brassica oleracea doubled haploid or inbred lines were performed. In total 3485 vital embryos have been obtained from 9514 pollinated buds. The success of interspecific hybridisation was highly depending on the maternal genotype (B. rapa) and ranged from 0 to 1.18 embryos per pollinated bud. For the genetic characterisation of the B. rapa and B. oleracea lines, a dendrogram was constructed based on 273 RAPD markers. Thus a well-characterised material is now available, which is suitable to analyse the effects of “fixed heterosis” and the interactions between homoeologous genes in allopolyploid species.