Genetic mapping and QTL analysis of fruit and flower related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

A set of 224 recombinant inbred lines (RILs) derived from a narrow cross between two fresh eaten types (S94 (Northern China type) × S06 (Northern European type)) (Cucumis sativus L.) was used to construct a genetic linkage map. With the RILs a 257-point genetic map was constructed including 206 SRAPs, 22 SSRs, 25 SCARs, 1 STS, and three economically important morphological markers (small spines (ss), uniform immature fruit color (u), dull fruit skin (D)). The seven linkage groups covered 1005.9 cM with a mean marker interval of 3.9 cM. The ss locus was linked to D and u, and they were all on Linkage group 6. The RIL map contained a total of 51 sequence-specific markers, which made possible the comparison of molecular linkage maps developed in different laboratories. Using the F_6:7 derived families, a total of 78 QTLs were detected with relatively high LOD scores (2.9–84.4) for nine fruit-related traits (fruit weight, length, and diameter, fruit flesh thickness, seed-cavity diameter, fruit-stalk length, fruit pedicel length, length/diameter and length/stalk ratio) and three flower-related traits (first flower node, first female flower node and female flower ratios). Several sequence-anchor markers (CSWCT25, CS30, CMBR41, CS08 etc.) were closely linked with some QTLs for fruit weight, fruit length, fruit flesh thickness and sex expression, which can be used for the future marker-assisted selection to improve the fruit traits in cucumber breeding. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. X. J. Yuan and J. S. Pan contributed equally to this investigation.     

A genetic linkage map of Spinacia oleracea and localization of a sex determination locus

A genetic map of Spinach (Spinacia oleracea) was constructed in a classical back cross population using 101 AFLP and 9 microsatellite markers. The map was divided into seven linkage groups with a total length of 585 cM and an average distance between the markers of 5.18 cM. The linkage map was constructed with LOD 3.5, but was quite stable with seven linkage groups remaining until LOD 7.0. Gender segregated 1 male to 1 female in the mapping population and was mapped to a small area of one linkage group with a distance of 1.9 cM to a microsatellite marker termed SO4. This small chromosomal region co-segregating with sex determination in the species is in contrast to previous reports on a heterologous XY chromosome system in spinach. Microsatellite markers used as anchors in the map construction were isolated from sequences of known nuclear encoded genes in spinach. This enabled simultaneous positioning on the map of these genes: Rubisco activase (Rca), Photosytem 1 subunit V (PsaG), Protein Kinase (Pk), Nitrate reductase (Nir), ferrodoxin:thioredoxin reductase (Ftr), Ribosomal protein L1 (Rps22), Choline monooxygenase (Cmo), Pseudogene for BZIP protein (Bzip), Glycerol-3-phosphate acyltransferase (Act1) and stromal ascorbate peroxidase, thylakoid-bound ascorbate peroxidase (Apx2). Spinach has a small genome, which makes it suitable for basic genomic studies and many physiologically important genes have been cloned from the species. The present map anchored with user friendly microsatellite markers will be useful for future studies of physiology and genetics of the species as well as studies of the nature of gender determination.     

QTL mapping of seedling traits in cucumber using recombinant inbred lines

Seedling traits are important for development, flower bud differentiation, fruit production and fruit quality of cucumber (Cucumis sativus L.). In this study, 160 recombinant inbred lines (RILs), derived from crossing wild cucumber inbred line PI 183967 (C. sativus var. hardwickii) with ‘931’ northern China cultivated cucumber inbred line 931, were employed to identify quantitative trait loci (QTLs) of cotyledon length (Cl), cotyledon width (Cw), hypocotyl length (Hl), first true leaf length (Fll), first true leaf width (Flw), aboveground fresh biomass (Afb) and aboveground dry biomass (Adb) at seedling stage. A genetic map including 307 SSR markers was developed which spanned 993.3 cM, with an average genetic distance of 3.23 cM between adjacent markers. 36 QTLs associated with the seven traits were detected on chromosomes 1, 2, 3, 5 and 6 in four environments (spring and autumn of 2012 and 2013), explaining 6.1 to 23.6% of the observed phenotypic variations. Among the 36 QTLs, 21 were responsible for more than 10% of observed phenotypic variations. We obtained 2, 2, 1 and 3 QTL loci for the traits of Fll, Flw, Afw and Adw, respectively. In addition, genes in the genetic region spanned by SSR15321‐SSR07711 on chr. 5 may contribute to Flw, Afw and Adw.     

Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)

Mottled/uniform color at the flower end of immature fruit is a highly important external quality trait that affects the market value of cucumber. Genetic analysis of different F₂ and backcross populations revealed that one single recessive gene, u (uniform immature fruit color), determines the uniform immature fruit color trait in cucumber. Based on earlier studies, the u locus is located on chromosome 5 (Chr. 5). By combining bulked segregant analysis using 60 published molecular markers on Chr. 5, we found that eight markers are polymorphic and are linked to the u locus. In addition, we developed five new relevant polymorphic simple sequence repeat (SSR) markers between markers SSR16203 and SSR15818. Subsequently, the F₂ population (477 individuals) from the cross of S06 (uniform fruit color line) × S94 (mottled fruit color line) was used for fine mapping of the u gene. The u gene was mapped to a 313.2-kb region between markers SSR10 and SSR27, at a genetic distance of 0.8 and 0.5 cM, respectively. Moreover, validity analysis of the codominant markers SSR10 and SSR27 was performed using 50 lines with mottled/uniform fruit color, demonstrating that these two SSR markers can be used for marker-assisted selection of the mottled/uniform fruit color trait in cucumber breeding. The results of this study will facilitate the cloning of the u gene.     

Genetic mapping of gummy stem blight (Didymella bryoniae) resistance genes in Cucumis sativus-hystrix introgression lines

Gummy stem blight (GSB, Didymella bryoniae (Auersw.) Rehm) is a devastating disease occurring worldwide in cucumber (Cucumis sativus L.) production and causing considerable yield loss. No commercially available cultivars are resistant to GSB. By screening 52 introgression lines (ILs) derived from the cross of C. hystrix × C. sativus and eight cucumber cultivar/lines through a whole plant assay, three ILs (HH1-8-1-2, HH1-8-5, HH1-8-1-16) were identified as GSB resistant lines. Six common introgression regions in these three ILs were on Chromosomes 1, 4, and 6. To further map the resistance in the ILs, three mapping populations (2009F₂, 2009F₂′ and 2010F₂) from a cross between resistant IL HH1-8-1-2 and susceptible 8419 were constructed and used for QTL mapping with SSR markers. Two quantitative trait loci (QTLs) were identified; one on Chromosome 4 and the other on Chromosome 6. The interval for Chromosome 4 QTL is 12 cM spanning 3.569 Mbp, and the interval for Chromosome 6 QTL is 11 cM covering 1.299 Mbp. The mapped QTLs provide a foundation for map-based cloning of the genes and establishing an understanding of the associated mechanisms underlying GSB resistance in cucumber.     

Stability of seed oil quality traits in high and mid-oleic acid sunflower hybrids

Powdery mildew caused by Podosphaera xanthii is an important disease of melon, and race 2F is the predominant race in most areas of China. Resistance to P. xanthii race 2F in melon K7-1 was controlled by a dominant gene, designated Pm-2F, in a 106-member population of recombinant inbred lines derived from K7-1× susceptible K7-2. Using bulked segregant analysis with molecular markers, we have identified two polymorphic simple sequence repeats (SSR) to determine that Pm-2F is located on linkage group II. Comparative genomic analyses using mapped SSR markers and the cucumber genome sequence showed that the melon chromosomal region carrying Pm-2F is homologous to a 288,223 bp genomic region on cucumber chromosome (chr) 1. The SSR markers on chr 1 of cucumber, SSR02734, SSR02733 and CS27 were found linked with Pm-2F. Comparative mapping showed that two SSR markers (SSR02734 and CMBR8) flanked the Pm-2F locus and two nucleotide binding site-leucine-rich repeat resistance genes were identified in the collinear region of cucumber. A cleaved amplified polymorphic sequence (CAPS) marker was developed from the sequence of resistance genes and it delimits the genomic region carrying Pm-2F to 0.8 cM. The evaluation of 165 melon accessions and 13 race differential lines showed that the newly developed CAPS (CAPS-Dde I) marker can be used as a universal marker for effective marker assisted selection in melon powdery mildew resistance breeding. The putative resistance gene cluster provides a potential target site for further fine mapping and cloning of Pm-2F.     

Identification and fine mapping of molecular markers closely linked to fruit spines size <Emphasis Type="Italic">ss</Emphasis> gene in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Fruit spine size is one of the importantly external quality traits effected the economic value of cucumber fruit. Morphological–cytological observation of the fruit spine size phenotype indicated that large spine formation arises from an increasing of spiny pedestal cell number caused by cell division, and best periods to accurately score fruit spine size trait was 4th day before flowering to 7th day after flowering according the continuous observation. Genetic analysis showed that a single dominant gene determined the fruit spine size trait in cucumber. BC₁ population (189 individuals) of two inbred lines (large spine PI197088 and small spine SA0422) was used for primary mapping of the SS/ss locus with 7 markers covering an interval of 37.1 cM. An F₂ segregating population of 1032 individuals constructed from the same two parents (PI197088 and SA0422) was used to fine mapping of the SS/ss locus. Six new markers linked to the gene were successfully screened for construction of a fine linkage map, in which the SS/ss locus was located in the region flanked by marker SE1 (3 recombinants) and SSR43 (2 recombinants) with a 189 kb physical distance. Markers from this study will be valuable for candidate gene cloning and marker-assisted selection for cucumber breeding.     

Molecular mapping and candidate gene analysis for fruit epidermal structure in cucumber

Firmness of skin is an important quality of processing cucumbers, which is a feature of the palisade epidermis in these types compared to flat epidermis in fresh cucumbers. This study was conducted to map the Pe (palisade epidermis) and analyse the candidate gene. Populations derived from the cross of two inbred lines, NCG122 with fruit flat epidermis and NCG121 with fruit palisade epidermis, were used to identify the inheritance of palisade epidermis and to map the gene involved in its development. The results showed that the palisade epidermis trait is controlled by a single gene, Pe, that is dominant over flat epidermis. Seven simple sequence repeat (SSR) and five insertion deletion (Indel) markers were identified to be linked to the Pe gene. It was mapped to cucumber chromosome 5 (Chr.5) between SSR14611 and Indelpe12 with genetic distances of 0.3 cM and 0.2 cM, respectively. The physical distance of the genomic region harbouring the gene was 227.5 kb with 26 predicted candidate genes. The accuracy of marker‐assisted selection using the molecular markers, Indelpe12 and SSR14611, was 68% and 88%, respectively.     

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 mapping of a stripe rust resistance gene in wheat cultivar Wuhan 2

Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat worldwide. Growing resistant cultivars is the best approach to control the disease. To identify and map genes for stripe rust resistance in wheat cultivar ‘Wuhan 2', an F₂ population was developed from a cross between the cultivar and susceptible cultivar Mingxian 169. The parents, 179 F₂ plants and their derived F_2:3 lines were evaluated for responses to Chinese races CYR30 and CYR31 of the pathogen in a greenhouse. A recessive gene for resistance was identified. DNA bulked segregant analysis was applied and resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to identify molecular markers linked to the resistance gene. A genetic map consisting of five RGAP and six SSR markers was constructed. The recessive gene, designated Yrwh2, was located on the short arm of chromosome 3B and flanked by SSR markers Xwmc540 and Xgwm566 at 5.9 and 10.0 cM, respectively. The chromosomal location of the resistance gene and its close marker suggest that the locus is different from previously reported stripe rust resistance genes Yr30, QYr.ucw-3BS, Yrns-B1, YrRub and QYrex.wgp-3BL previously mapped to chromosome 3B. Yrwh2 and its closely linked markers are potentially useful for developing stripe rust resistance wheat cultivars if used in combination with other genes.     

A high‐resolution einkorn (Triticum monococcum L.) linkage map involving wild,domesticated and feral einkorn genotypes

A high‐resolution consensus linkage map of Triticum monococcum was assembled from two separate maps involving domesticated, feral and wild einkorn wheat accessions. The genotyping‐by‐sequencing (GBS) approach based on DArTseq markers yielded overstretched maps. Deleting all markers with missing data and then converting dubious singletons to missing data produced two maps of about 1,380 cM, close to the published genome size. The consensus map spanned 1,562 cM, had one bin mapped every 0.92 cM and showed only one gap > 10 cM. Chromosome length varied between 151 cM (chromosome 4) and 270 cM (chromosome 7). The consensus map was compared to other A‐genome maps, and the sequences of genetically mapped DArTseq were used to anchor contigs of the T. monococcum, T. urartu and T. aestivum draft genomes based on sequence homology to assess colinearity and to assign mapped markers to the seven chromosomes of the bread wheat A‐genome. Finally, an in silico functional characterization of the sequences was performed. This high‐resolution map will facilitate QTL and association analysis and assist the genome assembly of the einkorn genome.     

Upregulation of polyphenol-related genes prevents ‘skin burning’ of well-colored ‘Cameo’ apples stored under stressful controlled atmosphere conditions

‘Skin burning’ of ‘Cameo’ apples resulting in poorly colored fruit can occur in storage under high CO₂ condition. To elucidate possible reasons for this physiological disorder, we assessed the differential expression of polyphenol-related genes. Poorly colored and well-colored mature ‘Cameo’ apples were stored under either high (3%) or low (0.7%) CO₂ levels, both in combination with 1% O₂, and monitored for seven months for ‘skin burning’. Samples were obtained by the end of storage period, and qPCR analyses were conducted using gene specific primers. We found expression levels of chalcone synthase (MdCHS), chalcone isomerase (MdCHI), anthocyanidin synthase (MdANS), flavonol synthase (MdFLS), dihydroflavonolreductase (MdDFR), and leucoanthocyanidinreductase (MdLAR1) genes to be substantially higher in well-colored compared to poorly colored apples. The delay in establishing the stressful controlled atmosphere (CA) storage condition (3% CO₂ level) led to significantly higher expression levels of MdLAR1, MdCHI, anthocyanidinreductase (MdANR) and flavanone 3-hydroxylase (MdF3H), which may explain the lower incidence of ‘skin burning’ by delayed CA fruit. On the other hand, after seven months in storage, the expression levels of phenylalanine ammonia-lyase (MdPAL), MdCHS, MdCHI, MdDFR, MdFLS, and MdF3H, were significantly higher in poorly colored injured apples, which reflect a feedback mechanism to synthesize more polyphenols to counteract the stressful storage condition.     

Molecular mapping re-locates the Stb2 gene for resistance to Septoria tritici blotch derived from cultivar Veranopolis on wheat chromosome 1BS

Septoria tritici blotch (STB) is one of the most destructive foliar diseases in many of the wheat (Triticum aestivum) growing regions of the world. Gene Stb2, derived from cultivar ‘Veranopolis’, provides effective resistance against STB. In our attempts to refine the map location of this resistance gene we could not confirm a previous report that Stb2 is on wheat chromosome 3BS. Instead, based on characterization of the same doubled-haploid population used for the original mapping derived from a cross between Veranopolis and susceptible line RAC875-2, and linkage analysis of the resistance phenotype to previously mapped SSR loci, we report that Stb2 is located on the short arm of wheat chromosome 1B, flanked by microsatellite loci Xwmc406 and Xbarc008 (with Xwmc230 closely located) at map distances of 6 and 5 cM, respectively. Presence of the markers on chromosome arm 1BS was confirmed by analysis of nullisomic-tetrasomic lines. These three co-dominant markers can be used in wheat breeding programs to facilitate combining Stb2 with genes of interest. Other STB resistance genes, including Stb11, have been reported on wheat chromosome arm 1BS, with locus Xbarc008 as a diagnostic marker. Whether Stb2, Stb11 and the previously identified Stb11-like genes are the same, allelic, or different but closely linked has not been determined. In addition to STB, numerous genes for resistance to many other fungal pathogens have been reported on wheat chromosome arm 1BS, including those for yellow (or stripe) rust, leaf rust and common bunt. The approximate locations for all of these genes were added onto the Stb2 map based on published distances from common markers to provide a rough guide for future wheat improvement.     

Genetic linkage map construction and location of QTLs for fruit-related traits in cucumber

A 173‐point genetic linkage map of cucumber (Cucumis sativus L.), consisting of 116 SRAPs, 33 RAPDs, 11 SSRs, 9 SCARs, 3 ISSRs, and 1 STS, was constructed using 130 F₂ progeny derived from a narrow cross between line S94 (Northern China open‐field type) and line S06 (greenhouse European type). The seven linkage groups spanned 1016 cM with a mean marker interval of 5.9 cM. Using the F₂ population and its F₃ derived families, a total of 38 QTLs were detected on five linkage groups with an LOD threshold of 3.0 for nine fruit‐related traits: fruit weight, length, and diameter, fruit flesh thickness, seed‐cavity diameter, fruit‐stalk length, fruit pedicel length, length/diameter and length/stalk ratio. Of the identified QTLs, fsl4.3 for fruit‐stalk length explained the largest portion of phenotypic variation (r² = ～30%). Several QTLs were detected in the same linkage region in different generations and different seasons. Additionally, several QTLs for various fruit traits were mapped to the same or neighbouring marker intervals, suggesting they are possible character associations for controlling cucumber fruit development.     

Identification of resistance gene analogue markers closely linked to wheat powdery mildew resistance gene Pm31

Specific oligonucleotide primers, designed for the sequences of known plant disease resistance genes, were used to amplify resistance gene analogues (RGAs) from wheat genomic DNA. This method was applied in a bulked segregant analysis to screen for the RGA markers linked to the powdery mildew resistance gene Pm31, introgressed into common wheat from wild emmer. Two RGA markers (RGA200 and RGA390) were found to be closely linked to Pm31 and completely co‐segregating with the marker allele of Xpsp3029 linked to Pm31, with a genetic distance of 0.6 cM. These two RGA markers were then integrated into the formerly established microsatellite map of Pm31 region. The result showed the effectiveness of the RGA approach for developing molecular markers linked to disease resistance genes and demonstrated the efficiency of denaturing polyacrylamide‐gel electrophoresis for detecting polymerase chain reaction polymorphism.     

QTL mapping of fruit nutritional and flavor components in tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis>) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross

Fruit nutritional and flavor components are important targets for breeding new cultivars of tomato (Solanum lycopersicum L.). We developed 108 recombinant inbred lines (the K39 RILs) in the F₆ generation from a cross between two phenotypically different breeding lines, K03 and K09. A linkage map was constructed using 172 genome-wide simple sequence repeat markers, 3 single-nucleotide polymorphism markers, and 2 phenotypic markers. The K39 RIL map consists of 12 linkage groups (LGs) and covers a genetic distance of 1089 cM. We measured the fruit soluble solids content (SSC), titratable acidity (TA), glutamic acid content (GLU), and lycopene content (LYC) of each line in four generations (F₆, F₈, F₁₀, F₁₁), β-carotene content (CAR) in two generations, and pH in one generation. By composite interval mapping that considered yearly variations in components as non-genetic effects, we detected three quantitative trait loci (QTLs) for SSC, four for TA, two for CAR, and one each for GLU, LYC, and pH. Among them, we found two QTLs for TA in LGs 6 and 11, those for GLU and LYC were candidates for novel QTLs. QTLs detected in this study were clustered in five LGs, but we observed no apparent trade-off relationships among the QTLs in each LG. Being derived from an intra-specific cross of tomato breeding materials, these QTLs can be used in practical breeding for improving fruit quality with low risk of linkage drag.     

Inheritances and location of powdery mildew resistance gene in melon Edisto47

Powdery mildew caused by Podosphaera xanthii is a major disease in melon. Here we report two Px race 1 strains named Px1A and Px1B in Xinjiang, which have different pathogenicities. The more pathogenic Px1B made some powdery mildew resistant genes on linkage group V (LGV) lose their resistant traits. The inheritances of resistance to Px1A and Px1B in melon Edisto47 were studied using a BC₁ population derived from a cross between the resistant genotype Edisto47 and the susceptible cultivar Queen. The resistance/susceptibility segregation ratios observed in the Px1A-inoculated BC₁ population and the loci of polymorphic markers indicated that resistance to Px1A was controlled by two dominant genes. Quantitative trait locus analysis identified two loci mapped on LGII and LGV, respectively, for powdery mildew resistance. However, for resistance to Px1B, Edisto47 was found to bear one dominant gene. A genetic linkage map was constructed using the Px1B-inoculated BC₁ population to map the resistant gene. Comparative genomic analyses revealed that the linkage map of Pm-Edisto47-1 was collinear with the corresponding genomic region of the melon chromosome 2. Genetic analysis showed that Pm-Edisto47-1 was located between simple sequence repeat (SSR) markers CMGA36 and SSR252089, at a genetic distance of 2.1 cM to both markers. Synteny analysis showed that two genes named MELO3C015353 and MELO3C015354 were predicted as candidates for Edisto47-1 in this region.     

QTLs for chlorophyll and chlorophyll fluorescence parameters in barley under post-flowering drought

Drought is one of the major factors limiting barley yields in many developing countries worldwide. The identification of molecular markers linked to genes controlling drought tolerance in barley is one way to improve breeding efficiency. In this study, we analyzed the quantitative trait loci (QTL) controlling chlorophyll content and chlorophyll fluorescence in 194 recombinant inbred lines (RILs) developed from the cross between the cultivar ‘Arta’ and Hordeum spontaneum 41-1. Five traits, chlorophyll content, and four chlorophyll fluorescence parameters, namely initial fluorescence (F_o), maximum fluorescence (F_m), variable fluorescence (F_v), and maximum quantum efficiency of PSII (F_v/F_m) which are related to the activity of the photosynthetic apparatus, were measured under well-watered and drought stress conditions at post-flowering stage. QTL analysis identified a total of nine and five genomic regions, under well-watered and drought stress conditions, respectively, that were significantly associated with the expression of the five target traits at post-flowering stage. No common QTL was detected except one for chlorophyll content, which was identified in both growth conditions, demonstrating that the genetic control of the expression of the traits related to photosynthesis differed under different water conditions. A QTL for F_v/F_m, which is related to the drought tolerance of photosynthesis was identified on chromosome 2H at 116 cM in the linkage map under drought stress. This QTL alone explained more than 15% of phenotypic variance of maximum quantum yield of PSII, and was also associated with the expression of four other traits. In addition, another QTL for F_v/F_m was also located on the same chromosome (2H) but at 135.7 cM explaining around 9% of the phenotypic variance under drought conditions. The result presented here suggest that two major loci, located on chromosome 2H, are involved in the development of functional chloroplast at post-flowering stage for drought tolerance of photosynthesis in barley under drought stress. If validated in other populations, chlorophyll fluorescence parameters could be used as selection criteria for drought tolerance.     

QTL mapping for anthocyanin and proanthocyanidin content in red rice

Anthocyanins and proanthocyanidins are the primary pigments of red rice and are also important functional nutrients for human health. To identify novel quantitative trait loci (QTLs) underlying anthocyanins and proanthocyanidins (ANC and PAC) in rice, a recombinant inbred line (RIL) derived from a cross of red rice ‘Hong Xiang 1’ (‘HX1’) and white rice ‘Song 98-131’ (‘S98-131’) was cultivated in six environments. A genetic map containing 126 markers covering 1833.4 cM with an average of 14.55 cM between markers was constructed. A total of 21 additive QTLs (A-QTLs) for ANC and PAC were identified from six environments using the IciMapping v3.3 software. Two new QTLs, qANC3 and qPAC12-4, were detected in several environments, and explained significant phenotypic variance. Nine QTLs of ANC and PAC were detected with additive × environmental interaction effects (AE effects) by QTLNetwork 2.1 software, but no epistatic and epistatic × environmental interaction effects (AA and AAE effects) were detected. The information obtained in this study could be useful for fine mapping and molecular marker-assisted selection of ANC and PAC in rice.     

High-density genetic map construction and QTL mapping for fiber strength on Chr24 across multiple environments in a CCRI70 recombinant inbred lines population

Upland cotton is an important economic crop that produces high-quality fiber for the textile industry. With the development of next-generation sequencing technology and improvements in human living standards, it has become possible to improve the fiber quality and yield of cotton with high-throughput molecular markers. Upland cotton 901-001 is an excellent, high-quality, non-transgenic cultivar, while the sGK156 strain shows high resistance to verticillium wilt. The phenotype of F₁ plants, certified in 2008 as national variety CCRI70, shows positive transgressive characteristics such as high quality, high yield, and resistance to verticillium wilt. We developed a population of 250 recombination inbred lines from a cross between 901-001 and sGK156. The fiber strength trait of plants from nine environments was collected, and a genetic linkage map of Chr24 comprising 168 SNP marker loci covering a genetic distance of 107.46 cM and with an average distance of 0.64 cM was generated. QTLs were identified across the nine environments using the composite interval mapping method. A total of eight QTLs for FS were identified on Chr24, three of which were stably expressed in at least five environments. Some candidate genes located in qFS-c24-2 and qFS-c24-4 were functionally annotated as potentially playing important roles in fiber development, with homologous genes reported in Arabidopsis thaliana. These results suggest that QTLs identified in the present study could contribute to improving FS and may be applicable for marker-assisted selection.