Efficient construction of high-density linkage map and its application to QTL analysis in barley

Using a High Efficiency Genome Scanning (HEGS) system and recombinant inbred (RI) lines derived from the cross of Russia 6 and H.E.S. 4, a high-density genetic map was constructed in barley. The resulting 1,595.7-cM map encompassed 1,172 loci distributed on the seven linkage groups comprising 1,134 AFLP, 34 SSR, three STS and vrs1 (kernel row type) loci. Including PCR reactions, gel electrophoresis and data processing, 6 months of work by a single person was sufficient for the whole mapping procedure under a reasonable cost. To make an appraisal of the resolution of genetic analysis for the 95 RI lines based on the constructed linkage map, we measured three agronomic traits: plant height, spike exsertion length and 1,000-kernel weight, and the analyzed quantitative trait loci (QTLs) associated with these traits. The results were compared on the number of detected QTLs and their effects between a high-density map and a skeleton map constructed by selected AFLP and anchor markers. The composite interval mapping on the high-density map detected more QTLs than the other analyses. Closely linked markers with QTLs on the high-density map could be powerful tools for marker-assisted selection in barley breeding programs and further genetic analyses including an advanced backcross analysis or a map-based cloning of QTL. Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by J.S. Heslop-Harrison     

Pleiotropic effect of a locus on chromosome 4 influencing alcohol drinking and emotional reactivity in rats

A QTL search in a segregating F2 intercross between HEP (High-Ethanol Preferring line) and wistar-kyoto (WKY, a low-alcohol consuming strain) rats identified a locus on chromosome 4 linked to the consumption of a 5% alcohol solution offered as a free choice with water (Terenina-Rigaldie et al. submitted). In order to confirm and analyse the influence of this locus, F2 rats were selected according to their genotype at the markers flanking the QTL and bred in order to obtain two groups of rats homozygous HEP/HEP ('HIGH' line) or WKY/WKY ('LOW' line) at the QTL, the rest of the genome being randomly inherited from one or the other founder strain. These two groups of animals displayed large differences in emotional reactivity (open field, elevated-plus maze), sensitivity to taste reinforcers (saccharin, quinine) and alcohol consumption (either forced or as a free choice with water). These results confirm the influence of this locus on alcohol intake and emotional reactivity traits, and suggest a pleiotropic effect of the gene(s) involved. Current research aims at the identification of this (these) gene(s).     

Location of genes involved in ear compactness in wheat (Triticum aestivum) by means of molecular markers

Quantitative trait loci (QTLs) for three traits related to ear morphology (spike length, number of spikelets, and compactness as the ratio between number of spikelets and spike length) in wheat (Triticum aestivum L.) were mapped in a doubled-haploid (DH) population derived from the cross between the cultivars Courtot and Chinese Spring. A molecular marker linkage map of this cross that had previously been constructed based on 187 DH lines and 380 markers was used for QTL mapping. The genome was well covered (85%) except chromosomes 1D and 4D and a set of anchor loci regularly spaced (one marker each 15.5 cM) were chosen for marker regression analysis. The presence of a QTL was declared at a significance threshold = 0.001. The population was grown in one location under field conditions during three years (1994, 1995 and 1998). For each trait, 4 to 6 QTLs were identified with individual effects ranging between 6.9% and 21.8% of total phenotypic variation. Several QTLs were detected that affected more than one trait. Of the QTLs 50% were detected in more than one year and two of them (number of spikelets on chromosome 2B, and compactness on chromosome 2D) emerged from the data from the three years. Only one QTL co-segregated with the gene Q known to be involved in ear morphology, namely the speltoid phenotype. However, this chromosome region explained only a minor part of the variation (7.5–11%). Other regions had a stronger effect, especially two previously unidentified regions located on chromosomes 1A and 2B. The region on the long arm of chromosome 1A was close to the locus XksuG34-1A and explained 12% of variation in spike length and 10% for compactness. On chromosome 2B, the QTL was detected for the three traits near the locus Xfbb121-2B. This QTL explained 9% to 22% of variation for the traits and was located in the same region as the gene involved in photoperiod response (Ppd2). Other regions were located at homoeologous positions on chromosomes 2A and 2D.     

Genetic analysis of rice CMS-WA fertility restoration based on QTL mapping

 The inheritance of fertility restoration of rice cytoplasmic male sterility of the wild abortive type was studied by means of QTL mapping. The two segregating populations examined showed high frequencies of highly sterile and highly fertile progenies, but a low frequency of partially sterile and partially fertile progenies. The distributions suggested that fertility restoration was mainly controlled by major genes. Based on a linkage map constructed with 57 RFLP and 61 AFLP markers on a B₁F₁ population, composite interval mapping (CIM) revealed that the fertility was restored by the additive effects of two restorer loci located on chromosome 10. One QTL, tightly linked to RFLP marker C1361 in the middle of the long arm of chromosome 10, explained 71.5% of the phenotypic variance. The second QTL was located between RFLP markers R2309 and RG257 on the short arm and explained 27.3% of the phenotypic variance. Similar results were obtained using the simple interval mapping (SIM) methods. Recived: 8 January 1998/Accepted: 22 April 1998     

Detection and analysis of QTLs for resistance to the brown planthopper, Nilaparvata lugens, in a doubled-haploid rice population

 We used a mapping population of 131 doubled-haploid lines, produced from a cross between an improved indica rice variety (IR64) and a traditional japonica variety (Azucena), to detect quantitative trait loci (QTLs) for resistance to the brown planthopper (BPH), Nilaparvata lugens. We evaluated the parents and mapping population with six tests that measure varying combinations of the three basic mechanisms of insect host plant resistance, i.e., antixenosis, antibiosis, and tolerance. To factor-out the effect of the major resistance gene Bph1 from IR64, the screening was done with two BPH populations from Luzon Island, The Philippines, that are almost completely adapted to this gene. A total of seven QTLs associated with resistance were identified, located on 6 of the 12 rice chromosomes. Individual QTLs accounted for between 5.1 and 16.6% of the phenotypic variance. Two QTLs were predominantly associated with a single resistance mechanism: one with antixenosis and one with tolerance. Most of the QTLs were derived from IR64, which has been shown to have a relatively durable level of moderate resistance under field conditions. The results of this study should be useful in transferring this resistance to additional rice varieties. Received: 10 May 1998 / Accepted: 4 June 1998     

Interval mapping of quantitative trait loci affecting NESTUR, a stem growth efficiency index of radiata pine seedlings

 NESTUR (needle-to-stem unit rate) is a stem growth index of conifer seedlings that measures the efficiency of stemwood production per unit of needle growth, and is related to other seedling traits such as height, stem diameter, stem volume and needle volume. Quantitative trait loci (QTLs) affecting the expression of stem growth efficiency in radiata pine seedlings were investigated using a RAPD linkage map constructed from markers scored on haploid, megagametophytic DNA. Four putative QTLs were detected which accounted for 8.5–36.4% of the population variance. A search for evidence of epistasis, using both complete pairwise and conditional interactions, did not yield any statistically significant result. Over a 3-year period, seedlings with high-NESTUR marker alleles showed a superior growth performance of 17–40% for height, diameter and volume over those with low-NESTUR marker alleles. Received: 10 July 1997 / Accepted: 31 March 1998     

Analyses of quantitative trait loci associated with resistance to shape Sclerotinia sclerotiorum in sunflowers (shape Helianthus annuus L.) using molecular markers

Restriction fragment length polymorphism and isoenzyme markers were used to investigate quantitative trait loci involved in sunflower resistance to mycelial extension of Sclerotinia sclerotiorum on leaves and capitula. Seed weight, oil content and flowering data were also evaluated. Four quantitative trait loci were demonstrated for leaf resistance and two for capitulum resistance. One of these zones appears involved in resistance to both types of S. sclerotiorum attack while the others appear specific for resistance of one part of the plant. Two quantitative trait loci were detected for seed weight, three for oil content and three for flowering date. Individual quantitative trait loci explained 9% to 48% of the phenotypic variability, confirming the polygenic basis of the quantitative traits studied. Overall, the quantitative trait loci explain 60% of the genetic variation for leaf resistance and 38% for capitulum resistance to S. sclerotiorum. One linkage group is particularly interesting since it includes quantitative trait loci for all the five quantitative traits measured. Hypotheses for linkage versus pleiotropy and consequences of all the results in resistance breeding are discussed.     

Effects of the Menopause Transition on Body Fatness and Body Fat Distribution

Objective : The menopause transition increases cardiovascular and metabolic disease risk, partly because of the adverse effects of estrogen deficiency on the plasma lipid-lipoprotein profile and cardiovascular function. This increased cardiovascular and metabolic disease risk may also be partially mediated by increased body fat, increased intraabdominal adipose tissue accumulation, or both. The objective of this mini-review is to summarize studies that have investigated the relationships among the menopause transition, body fatness, and body fat distribution. Research Methods and Procedures : A review of cross-sectional and longitudinal studies on menopause that examined body fatness and body fat distribution. Results : Cross-sectional reports show that the menopause transition is related to modest increases in body mass index or total fatness, although not all studies found significant effects. Increased central adiposity appears to be related to menopause, independent of advancing age, but these results are methodology dependent. An independent effect of menopause on central body fatness was noted by the use of techniques such as DEXA or computed tomography, whereas studies using circumference measures showed discrepant results. Longitudinal studies showed that the menopause transition accelerated the increase in central adiposity, although no studies quantified changes in intra-abdominal fat by imaging techniques. Discussion : Thus, additional longitudinal studies using more accurate measures of adiposity are needed to critically examine the effects of the menopause transition on total and central body fatness. Collectively, previous studies suggest that menopause is related to modest increase in total fatness and accelerated accumulation of central body fat that exceeds changes normally attributed to the aging process. These changes may increase the risk for cardiovascular and metabolic disease in aging women.     

Four QTL in Rice Associated with Broad Spectrum Resistance to Blast Isolates from Rice and Barley

Pyricularia grisea is the most destructive and cosmopolitan fungal pathogen of rice and it can also cause disease on other agriculturally important cereals. We determined the number, location and interaction of quantitative trait loci (QTL) associated with resistance to P. grisea isolates obtained from rice (THL142 and THL222) and barley (TH16 and THL80) grown in Thailand. The isolates showed a spectrum of virulence when used to inoculate a series of differentials. We used a reference blast resistance mapping population of rice (IR64 × Azucena). IR64 was highly resistant, and Azucena was highly susceptible, to all four isolates. The numbers of resistant vs. susceptible progeny suggest that the resistance of IR64 is determined by two or three genes with additive effects. The correlation coefficients for all pairwise comparisons of disease severity were high and highest between barley isolates and between rice isolates. Four QTL were detected, one on each of the following chromosomes 2, 8, 9 and 10. IR64 contributed resistance alleles at three of the QTL (chromosomes 2, 8 and 9). Azucena contributed the resistance allele at the QTL on chromosome 10 in response to inoculation with isolate THL142. The results of the QTL analysis support interpretation of the phenotypic frequency distributions regarding the number of genes determining resistance to the four isolates in this population. Our results are novel in adding blast isolates from barley to the catalogue of pathogen specificities to which a gene, or genes, from IR64 confer resistance.     

水稻蒸煮品质相关QTL定位及候选基因分析

挖掘与稻米蒸煮品质相关的数量性状基因座(quantitative trait locus, QTL)，分析候选基因，并通过遗传育种手段改良稻米蒸煮品质相关性状，可有效提升稻米的口感。以籼稻华占(Huazhan, HZ)、粳稻热研2号(Nekken2)及由其构建的120个重组自交系(recombinant inbred lines, RILs)群体为实验材料，测定成熟期稻米的糊化温度(gelatinization temperature, GT)、胶稠度(gel consistency, GC)和直链淀粉含量(amylose content, AC)。结合高密度分子遗传图谱进行QTL定位，共检测到26个与稻米蒸煮品质相关的QTLs (糊化温度相关位点1个、胶稠度相关位点13个、直链淀粉含量相关位点12个)，其中最高奇数的可能性(likelihood of odd, LOD)值达30.24。通过实时荧光定量PCR (quantitative real-time polymerase chain reaction, qRT-PCR)分析定位区间内候选基因的表达量，发现6个基因在双亲间的表达量差异显著，推测LOC_Os04g20270和LOC_Os11g40100的高表达可能会极大地提高稻米的胶稠度，而LOC_Os01g04920和LOC_Os02g17500的高表达以及LOC_Os03g02650和LOC_Os05g25840的低表达有助于降低直链淀粉含量。这些结果为培育优质水稻新品种奠定了分子基础，并为揭示稻米蒸煮品质的分子调控机制提供了重要的遗传资源。