Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species

Quantitative trait loci (QTLs) for several fruit traits in tomato were mapped and characterized in a backcross population of an interspecific cross between Lycopersicon esculentum fresh-marker breeding line NC84173 and L. pimpinellifolium accession LA722. A molecular linkage map of this cross that was previously constructed based on 119 BC1 individuals and 151 RFLP markers was used for the QTL mapping. The parental lines and 119 BC1S1 families (self-pollinated progeny of BC1 individuals) were grown under field conditions at two locations, Rock Spring, PA, and Davis, CA, and fruits were scored for weight (FW), polar (PD) and equatorial diameters (ED), shape (FS), total soluble solids content (SSC), pH and lycopene content (LYC). For each trait, between 4 and 10 QTLs were identified with individual effects ranging between 4.4% and 32.9% and multilocus QTL effects ranging between 39% and 75% of the total phenotypic variation. Most QTL effects were predictable from the parental phenotypes, and several QTLs were identified that affected more than one trait. A few pairwise epistatic interactions were detected between QTL-linked and QTL-unlinked markers. Despite great differences between PA and CA growing conditions, the majority of FW QTLs (78%) and SSC QTLs (75%) in the two locations shared similar genomic positions. Almost all of the QTLs that were identified in the present study for FW and SSC were previously identified in six other studies that used different interspecific crosses of tomato; this indicates conservation of QTLs for fruit traits across tomato species. Altogether, the seven studies identified at least 28 QTLs for FW and 32 QTLs for SSC on the 12 tomato chromosomes. However, for each trait a few major QTLs were commonly identified in 4 or more studies; such ‘popular’ QTLs should be of considerable interest for breeding purposes as well as basic research towards cloning of QTLs. Notably, a majority of QTLs for increased SSC also contributed to decreased fruit size. Therefore, to significantly increase SSC of the cultivated tomato, some compromise in fruit size may be unavoidable. This revised version was published online in June 2006 with corrections to the Cover Date.     

Identification of QTLs with additive,epistatic and QTL × development interaction effects for seed dormancy in rice

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.     

Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings

Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (G_max), germination rate (t₅₀) and uniformity (U₈₄₁₆) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.     

A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat

Key message

A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number.

Abstract

Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between ‘20828’ and ‘Chuannong16’ was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23–45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of ‘Chinese Spring’ and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work.

     

Accumulation of the β-subunit of polygalacturonase 1 in normal and mutant tomato fruit

Polyclonal antiserum raised against the native PG1 isoform of tomato fruit (Lycopersicon esculentum Mill.) polygalacturonase [poly(1,4--d-galacturonide) glycanohydrolase, EC 3.2.1.15] bound to each of the subunits of the protein and also to a range of other fruit proteins. Affinity purification was used to remove antibody molecules that bound to the native form of the PG2 isoform. The resulting serum bound to native PG1, denatured PG2 and -subunits of PG1 but not to native PG2 or other fruit proteins. This anti-PG1 serum was used to monitor the occurrence of the PG1 -subunit and PG2 in detergent extracts of tomato tissues. The -subunit polypeptide was detected in pericarp but not locule tissue of fruit, including fruit of the rin and nor mutants. It increased in amount in the pericarp tissues from an early stage to the mature green stage, clearly prior to any appreciable accumulation of the PG2 subunit. The -subunit polypeptide was not detected in stem or leaf tissues. A PG2-specific antiserum was used to study the interaction of PG2 with the isolated -subunit. The PG2 isoform was bound to the -subunit over a wide range of salt concentrations and pH; the interaction was independent of the presence of reducing agents. It is concluded that strong non-covalent forces are involved in the interaction. The results are consistent with a model in which the -subunit is positioned in the cell wall structure and provides a specific binding site for the active PG2 subunit when this is synthesised during ripening.Abbreviations B breaker - MG mature green - M_r relative molecular mass - nor non-ripening mutant - PAGE polyacrylamide gel electrophoresis - PG polygalacturonase - rin ripening inhibitor mutant - SDS sodium dodecyl sulphate     

Constitutive overexpression of a ripening-related pepper endo-1,4-β-glucanase in transgenic tomato fruit does not increase xyloglucan depolymerization or fruit softening

The ripening-related pepper endo-1,4--D-glucanase (EGase) CaCel1 was over-expressed in transgenic tomato plants under the control of the constitutive 35S promoter to investigate the effects on plant growth and fruit softening of high levels of a potential cell wall-degrading activity. In transgenic fruit, recombinant CaCel1 protein was associated with a high-salt putative cell wall fraction, and extractable CMCase activity was increased by up to 20-fold relative to controls. However, the effects of high levels of EGase activity on fruit cell wall metabolism were relatively small. The largest consequence observed was a decrease of up to 20% in the amount of matrix glycans in a 24% KOH-soluble fraction consisting of polysaccharides tightly bound to cellulose. This decrease was confined to polysaccharides other than xyloglucan, did not affect the size distribution of remaining molecules, and was not correlated with a corresponding increase in glycans in a 4% KOH-soluble fraction loosely bound to cellulose, suggesting that the missing polymers had been degraded to fragments small enough to be lost from the extracts. The amount of matrix glycans in the 4% KOH-soluble fraction was not substantially changed, but the size distribution showed a small relative increase in the amount of polymers in a peak eluting close to a linear dextran marker of 71 kDa. This could be due either to an increase in the amount of polymers of this size, or to a loss from the extract of other polymers present in peaks of higher molecular weight. Transgenic fruit were not softer than controls but appeared the same or slightly firmer at both green and red developmental stages, and no differences in plant vegetative growth were observed. CaCel1 did not cause depolymerization of tomato fruit xyloglucan in vivo, but differences in the amount or molecular weight profile of other matrix glycans were observed. The data suggest that degradation of a proportion of matrix glycans other than xyloglucan does not result in fruit softening, and that fruit softening is not limited by the amount of EGase activity present during ripening.     

QTL mapping for grain filling rate and yield-related traits in RILs of the Chinese winter wheat population Heshangmai × Yu8679

A set of 142 winter wheat recombinant inbred lines (RILs) deriving from the cross Heshangmai x Yu8679 were tried in four ecological environments during the seasons 2006 and 2007. Nine agronomic traits comprising mean grain filling rate (GFR(mean)), maximum grain filling rate (GFR(max)), grain filling duration (GFD), grain number per ear (GNE), grain weight per ear (GWE), flowering time (FT), maturation time (MT), plant height (PHT) and thousand grain weight (TGW) were evaluated in Beijing (2006 and 2007), Chengdu (2007) and Hefei (2007). A genetic map comprising 173 SSR markers and two EST markers was generated. Based on the genetic map and phenotypic data, quantitative trait loci (QTL) were mapped for these agronomic traits. A total of 99 putative QTLs were identified for the nine traits over four environments except GFD, PHT and MT, measured in two environments (BJ07 and CD07), respectively. Of the QTL detected, 17 for GFR(mean), 16 for GFR(max), 21 for TGW and 10 for GWE involving the chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5B, 6D and 7D were identified. Moreover, 13 genomic regions showing pleiotropic effects were detected in chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4B, 4D, 5B, 6D and 7D; these QTL revealing pleiotropic effects may be informative for a better understanding of the genetic basis of grain filling rate and other yield-related traits, and represent potential targets for multi-trait marker aided selection in wheat.     

Genetic control of estrogen action in the rat: mapping of QTLs that impact pituitary lactotroph hyperplasia in a BN × ACI intercross

Estrogens are important regulators of growth and development and contribute to the etiology of several types of cancer. Different inbred rat strains exhibit marked, cell-type-specific differences in responsiveness to estrogens as well as differences in susceptibility to estrogen-induced tumorigenesis. Regulation of pituitary lactotroph homeostasis is one estrogen-regulated response that differs dramatically between different inbred rat strains. In this article we demonstrate that the growth response of the anterior pituitary gland of female ACI rats to 17β-estradiol (E2) markedly exceeds that of identically treated female Brown Norway (BN) rats. We further demonstrate that pituitary mass, a surrogate indicator of absolute lactotroph number, behaves as a quantitative trait in E2-treated F₂ progeny generated in a genetic cross originating with BN females and ACI males. Composite interval mapping analyses of the (BN×ACI)F₂ population revealed quantitative trait loci (QTLs) that exert significant effects on E2-induced pituitary growth on rat chromosome 4 (RNO4) (Ept5) and RNO7 (Ept7). Continuous treatment with E2 rapidly induces mammary cancer in female ACI rats but not BN rats, and QTLs that impact susceptibility to E2-induced mammary cancer in the (BN×ACI)F₂ population described here have been mapped to RNO3 (Emca5), RNO4 (Emca6), RNO5 (Emca8), RNO6 (Emca7), and RNO7 (Emca4). Ept5 and Emca6 map to distinct regions of RNO4. However, Ept7 and Emca4 map to the same region of RNO7. No correlation between pituitary mass and mammary cancer number at necropsy was observed within the (BN×ACI)F₂ population. This observation, together with the QTL mapping data, indicate that with the exception of the Ept7/Emca4 locus on RNO7, the genetic determinants of E2-induced pituitary growth differ from the genetic determinants of susceptibility to E2-induced mammary cancer.     

Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula

Freezing is a major environmental limitation to crop productivity for a number of species including legumes. We investigated the genetic determinism of freezing tolerance in the model legume Medicago truncatula Gaertn (M. truncatula). After having observed a large variation for freezing tolerance among 15 M. truncatula accessions, the progeny of a F6 recombinant inbred line population, derived from a cross between two accessions, was acclimated to low above-freezing temperatures and assessed for: (a) number of leaves (NOL), leaf area (LA), chlorophyll content index (CCI), shoot and root dry weights (SDW and RDW) at the end of the acclimation period and (b) visual freezing damage (FD) during the freezing treatment and 2 weeks after regrowth and foliar electrolyte leakage (EL) 2 weeks after regrowth. Consistent QTL positions with additive effects for FD were found on LG1, LG4 and LG6, the latter being the most explanatory (R ² ≈ 40 %). QTL for NOL, QTL for EL, NOL and RDW, and QTL for EL and CCI colocalized with FD QTL on LG1, LG4 and LG6, respectively. Favorable alleles for these additive effects were brought by the same parent suggesting that this accession contributes to superior freezing tolerance by affecting plants’ capacity to maintain growth at low above-freezing temperatures. No epistatic effects were found between FD QTL, but for each of the studied traits, 3–6 epistatic effects were detected between loci not detected directly as QTL. These results open the way to the assessment of syntenic relationships between QTL for frost tolerance in M. truncatula and cultivated legume species.     

Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population II: conventional QTL analysis

Modifying plant root systems is considered a means of crop improvement targeted to low-resource environments, particularly low nutrient and drought-prone agriculture. The identification of quantitative trait loci (QTLs) for root traits has stimulated marker-assisted breeding to this end, but different QTLs have been detected in different populations of the same species, and importantly, in the same population when grown in different experimental environments. The presence of QTL × environment interaction is implicated, and this must be characterised if the utility of the target QTLs is to be realised. Previous attempts to do this suffer from a lack of control over replicate environments and inadequate statistical rigour. The Bala × Azucena mapping population was grown in two replicate experiments of four treatment environments, a control, a low light, a low soil nitrogen and a low soil water treatment. After a 4 weeks growth, maximum root length, maximum root thickness, root mass below 50 cm, total plant dry mass, % root mass and shoot length were measured. A summary of the overall results is presented in an accompanying paper. Here, QTL analysis by composite interval mapping is presented. A total of 145 QTLs were detected, mapping to 37 discrete loci on all chromosomes. Superficial evidence of QTL × E (great difference in LOD score) was tested by single-marker analysis which confirmed QTL × E for five loci representing only five individual trait-loci interactions. Some loci appeared to be stable across environments. Some QTLs were clearly more or less active under low light, low nitrogen or drought. A few notable loci on chromosomes 1, 2, 3, 5, 7 and 9 are briefly discussed. Also discussed are some remaining statistical shortcomings that will be addressed in another companion paper.     

Q- and C-band polymorphism of the chromosomes in a group of patients with the Shereshevski?-Turner syndrome

Q- and C-band polymorphism of heterochromatic regions of chromosomes were studied in a group of patients with Turner's syndrome (30 girls with the karyotype 45, X) and in 105 normal individuals. No significant differences in the frequencies of Q-polymorphic variants for the most part of chromosomes studied (with the exception of chromosome 13 satellites) were obtained between patients with Turner's syndrome and the control. There were no differences in the mean number of Q-variants per individual in both groups investigated. An increase in the frequency of large C-segments of chromosome 9 was detected in patients with Turner's syndrome. An increase in the frequency of individuals carrying a combination of several extreme variants in the individual karyotype was found for patients with Turner's syndrome. The differences revealed are of non-specific character for a given form of developmental pathology.     

A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map

The cultivated strawberry, Fragaria × ananassa, is the most economically-important soft-fruit species, but few practical molecular tools for the purpose of marker assisted selection currently exist. As a precursor to the development of such tools, a genetic linkage map was developed from a F₁ population comprising 174 seedlings derived from a cross between two F. × ananassa cultivars, ‘Redgauntlet’ × ‘Hapil’. The resultant map is composed of 315 molecular markers—218 microsatellites, 11 gene-specific markers and 86 AFLP and RAPD markers—and spans 3,116 cM. In total, 69 linkage group fragments were recovered, more than the 56 linkage groups expected for the cultivated strawberry, however, all fragments contained a transferable marker that could be associated with one of 56 linkage group scaffolds. The female (Redgauntlet) and male (Hapil) linkage maps are composed, respectively of 170 loci in 32 linkage groups covering 1,675.3 cM and 182 loci in 37 linkage groups covering 1,440.7 cM, with 37 markers common to both maps. The maximum number of markers in one linkage group was 15, the minimum was two. All linkage groups resolved contained at least one transferable marker (SSR or gene-specific) that had been mapped on the diploid Fragaria reference map (FV × FB), and therefore all linkage groups could be identified as homologous to one of the seven diploid Fragaria linkage groups. When marker order was compared to the diploid Fragaria reference map, effectively complete colinearity was observed. However, the occurrence of duplicated loci on homologues of linkage groups FG1 and FG6 provided evidence of a putative chromosomal duplication or translocation event in Fragaria. The development of this linkage map will facilitate the study and dissection of QTL associated with traits of economic importance such as disease resistance and fruit quality, and provides a foundation for the development of markers for the purpose of marker assisted breeding and selection in the cultivated strawberry, F. × ananassa.     

Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice

A quantitative trait locus (QTL) associated with the protein content of cytosolic glutamine synthetase (GS1; EC 6.3.1.2) in senescing leaves, panicle number, and panicle weight was characterized in rice (Oryza sativa L.). A near-isogenic line (NIL), C-22, developed by marker-assisted selection was grown under different nitrogen levels in the greenhouse and in a paddy field. Chromosome 2 of C-22 had an approximately 50-cM segment substituted from the Kasalath (indica) chromosome in a Koshihikari (japonica) genetic background. C-22 showed a 12–37% lower content of GS1 protein in leaf blades than Koshihikari, which was in good agreement with a QTL region positively affected by the japonica chromosome. At an early vegetative stage, C-22 had more active tillers than Koshihikari in the greenhouse. At the reproductive stage, both panicle number and total panicle weight of C-22 were significantly higher than those of Koshihikari, particularly when the plants were grown under a low-nitrogen condition. These traits of C-22 were further confirmed in a paddy field. Thus, tiller development was positively affected by the Kasalath chromosome at an early vegetative stage, which resulted in an increased panicle number and panicle weight at the mature stage in C-22. These data indicate that the target QTL (Pnn1; panicle number 1) is important in the development of tillers and panicles in rice. Linkage analyses for panicle number and ratio of developing tiller formation in the second axil (RDT) revealed that Pnn1 was delimited at the 6.7-cM region.     

Genetic mapping and QTL analysis for yield and agronomic traits with an F2:3 population derived from a waxy corn × sweet corn cross

We constructed a framework map using SSR markers in the F₂ population derived from a cross between a waxy corn inbred line and a sweet corn inbred line. We constructed a genetic linkage map of the F_2:3 population employing 295 SSR markers on 158 F₂ individuals produced from the cross. The map comprised a total genomic length of 2,626.5 cM in 10 linkage groups and an average distance between markers of 8.9 cM. The number of loci per linkage group ranged from 27 (chr. 5) to 34 (chr. 7). The genetic distance per linkage group ranged from 213.6 cM (chr. 10) to 360.6 cM (chr. 2). Χ ² tests revealed that 254 markers (86.1 %) distributed over all 10 chromosomes exhibited a Mendelian segregation ratio of 1:2:1. A total of 14 quantitative trait loci (QTLs) for days to silking (DTS), plant height (PH), ear height (EH), ear height ratio (ER), ear length (L-ear), and setted ear length (L-sear) were found in the 158 F₂ progeny. They were mapped to chromosomes 1, 2, 3, 7, 8, and 10. Among them, one QTL was associated with DTS, three with PH, six with EH, one with ER, two with L-ear, and one QTL was related to L-sear. In our study, we found that four QTLs: qDTS1, qEH1a, qEH1b, and qPH1, were clustered between umc2390 and umc1603 on chromosome 1. These new QTLs identified by the present study could serve as useful molecular markers in selecting for yield and agronomic traits in maize. The results of this study may improve the identification and characterization of genes responsible for yield and agronomic traits in waxy corn and sweet corn.     

Genetic mapping of a major codominant QTL associated with β-carotene accumulation in watermelon

The common flesh color of commercially grown watermelon is red due to the accumulation of lycopene. However, natural variation in carotenoid composition that exists among heirloom and exotic accessions results in a wide spectrum of flesh colors. We previously identified a unique orange flesh watermelon accession (NY0016) that accumulates mainly β-carotene and no lycopene. We hypothesized this unique accession could serve as a viable source for increasing provitamin A content in watermelon. Here we characterize the mode of inheritance and genetic architecture of this trait. Analysis of testcrosses of NY0016 with yellow and red fruited lines indicated a codominant mode of action as F₁ fruits exhibited a combination of carotenoid profiles from both parents. We combined visual color phenotyping with genotyping-by-sequencing of an F_2:3 population from a cross of NY0016 by a yellow fruited line, to map a major locus on chromosome 1, associated with β-carotene accumulation in watermelon fruit. The QTL interval is approximately 20 cM on the genetic map and 2.4 Mb on the watermelon genome. Trait-linked marker was developed and used for validation of the QTL effect in segregating populations across different genetic backgrounds. This study is a step toward identification of a major gene involved in carotenoid biosynthesis and accumulation in watermelon. The codominant inheritance of β-carotene provides opportunities to develop, through marker-assisted breeding, β-carotene-enriched red watermelon hybrids.     

SAR versus VAR, and the size and shape that provide the most appropriate RF exposure metric in the range of 0.5-6 GHz

Basic restrictions for protecting against localized tissue heating induced from exposure to radiofrequency (RF) fields are typically specified as the specific energy absorption rate (SAR), which is mass averaged in recognition of the thermal diffusion properties of tissues. This article seeks to determine the most appropriate averaging mass (1, 3, 5, 7, or 10 g) and averaging shape (cube or sphere). We also consider an alternative metric, volumetric energy absorption rate (VAR), which uses volume averaging (over 1, 3, 5, 7, and 10 cm³; cube and sphere). The SAR and VAR averaging approaches were compared by considering which was a better predictor of tissue temperature rise (ΔT) induced by near‐ and far‐field RF exposures (0.5–6 GHz), calculated in a detailed human body model. For the exposure scenarios that we examined, VAR is better correlated with ΔT than SAR, though not at a statistically significant level for most of the metric types we studied. However, as VAR offers substantive advantages in ease of assessment we recommend this metric over SAR. Averaging over a cube or a sphere provides equivalent levels of correlation with ΔT, and so we recommend choosing the averaging shape on the basis of which is easier to assess. The optimal averaging volume is 10 cm³ for VAR, and the optimal mass is 10 g for SAR. The correlation between VAR or SAR and ΔT diminishes substantially at 6 GHz, where incident power flux density may be a better exposure metric. Bioelectromagnetics 32:312–321, 2011. © 2010 Wiley‐Liss, Inc.     

QTL for fibre-related traits in grain × sweet sorghum as a tool for the enhancement of sorghum as a biomass crop

Compared to maize and temperate grasses, sorghum has received less attention in terms of improving cell wall components. The objectives of this study were to identify quantitative trait loci (QTL) with main effects, epistatic and pleiotropic effects along with QTL × environment (QE) interactions controlling fibre-related traits in sorghum. Neutral detergent fibre (NDF), acid detergent fibre (ADF), acid detergent lignin (ADL), cellulose, hemicellulose, fresh leaf mass, stripped stalk mass, dry stalk mass, fresh biomass and dry biomass were analysed from a population of 188 grain × sweet sorghum recombinant inbred lines. A genetic map consisting of 157 DNA markers was constructed, and QTL were detected using composite interval mapping (CIM). CIM detected more than 5 additive QTL per trait explaining 7.1–24.7% of the phenotypic variation. Abundant co-localization of these QTL was observed across all chromosomes, and the highest cluster was identified on chromosome 6. Searching for candidate genes using the confidence interval of our QTL clusters reveals that these clusters might comprise a set of genes that are tightly linked. Some QTL showed multiple effects; however, the allele for each trait was favouring the parent with the increasing effect. QE interactions were observed for QTL showing multiple effects. Additive × additive interaction was observed for 7 out of 10 traits, indicating the importance of epistatic analysis. However, the phenotypic variation explained by digenic interactions was lower compared to the individual QTL. Our results indicate that various genetic components contribute to fibre-related traits and should be considered during the enhancement of sorghum for lignocellulosic biomass.     

Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence

Capsicum spp. are widely cultivated for use as vegetables and spices. The Kihara Institute for Biological Research, Yokohama City University, Japan, has stocks of approximately 800 lines of Capsicum spp. collected from various regions of Central and South America, the regions of origin for Capsicum spp. In this study, 5,751 primer pairs for simple sequence repeat markers, based on 118,060 publicly available sequences of expressed sequence tags of Capsicum annuum, were designed and subjected to a similarity search against the genomic sequence of tomato, a model Solanaceae species. Nucleotide sequences spanning 2,245 C. annuum markers were successfully mapped onto the tomato genome, and 96 of these, which spanned the entire tomato genome, were selected for further analysis. In genotyping analysis, 60 out of the 77 markers that produced specific DNA amplicons showed polymorphism among the Capsicum lines examined. On the basis of the resulting data, the 192 tested lines were grouped into five main clusters. The additional sequencing analysis of the plastid genes, matK and rbcL, divided the resources into three groups. As a result, 19 marker loci exhibited genotypes specific to species and cluster, suggesting that the DNA markers are useful for species identification. Information on the DNA markers will contribute to Capsicum genetics, genomics, and breeding.