Combination Of Quantitative Trait Loci Research Articles

Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping.

Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging. In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions. By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1. By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Marker assisted pyramiding of qDTY QTLs governing yield under drought stress into rice variety ADT(R)45

Drought occurrence during reproductive stage of rice leads to significant yield loss. Rice production has to be doubled to feed the ever increasing human population. As the yield levels are stagnated under favourable production system, improvement of yield under unfavourable environment is key to attain the projected target. Therefore, the present study was undertaken to improve the drought tolerance of popular rice variety ADT(R)45 by introgressing major effect quantitative trait loci (QTLs) conferring yield under drought (qDTY1.1, qDTY3.1 and qDTY12.1) through marker assisted backcross breeding (MABB). Through MABB, 117 BILs in the background of ADT(R)45 were developed with different combinations of qDTY QTLs.  The BILs were evaluated under rainfed target production environment and observations on nine biometrical and yield traits were recorded. Variability analysis revealed presence of additive gene action for the traits viz., total number of tillers per plant, number of productive tillers per plant, hundred grain weight, yield per hectare and single plant yield. Hence, selection based on these traits will be effective to improve yield under drought stress. Association analysis showed total number of tillers per plant, number of productive tillers per plant, panicle length, hundred grain weight and spikelet fertility percentage were highly correlated with yield per plant. Comparison of BILs with different QTL combinations showed that BILs with single QTL (qDTY12.1) was better for most of the traits studied. BILs with single or two QTL combinations were found to perform better under rainfed condition, when compared to BILs with all the three QTLs. Keywords: Reproductive stage drought, Rainfed, qDTYs, rice, BILs, MABB

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster.

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109.

Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.

Construction of a high-density genetic map using specific-length amplified fragment markers and identification of QTLs for branching angle in poplar.

Branching angle is a critical factor that determines the morphological establishment and is a typical quantitative trait controlled by multiple genes. In this study, we used SLAF-seq to construct a high-density genetic map, to investigate the genetic architecture of branching angle in poplar (Populus leucopyramidalis). A total of 240,672 SLAF tags were obtained, including 103,691 polymorphic SLAF tags. After filtering, 53,407 polymorphic markers were sorted into eight segregation types, and 11,162 of them were used to construct the genetic map. 8447 were on the female parent map, 8532 were on the male parent map, and 11,162 were on the integrated map. The marker coverage was 4820.84 and 5044.80cM for the female and male maps, and 3142.61cM for the integrated map. The average intervals between two adjacent mapped markers were 0.55, 0.59, and 0.28cM for the three maps, respectively. Two quantitative trait loci (QTLs) were detected. Seven markers that exceeded the threshold in these two regions were considered as being associated with branching angle and the phenotypic variance explained by each of these marker was 10.64-11.66%. After functional annotation, we identified 15 candidate genes and analyzed the expression of candidate genes in narrow and wide crown progenies by qRT-PCR. These results show that the combination of QTL and SLAF-seq will contribute to future breeding plans in poplar breeding, especially in narrow crown poplar breeding.

Improvement of grain yield under moisture and heat stress conditions through marker-assisted pedigree breeding in rice (

Enhancement of rice (Oryza sativa L.) productivity under rainfed ecosystems is important to food security. Efforts to increase yield have had little success, mainly due to the complexity of inheritance of abiotic stress tolerance traits and the technical challenges of phenotyping these traits. The study was conducted to pyramid quantitative trait loci (QTLs) governing tolerance to moisture and heat stress from cv. Nagina22 and QTLs for high yield traits from variety IR64, with the aid of marker-assisted pedigree breeding. From the IR64/N22 cross, we identified 14 pyramided lines with various combinations of targeted QTLs (5–11 QTLs). The three best lines that performed well under moisture stress conditions were PL76 with two water-use efficiency (WUE) QTLs (Mr19a, SLA 9.1), three drought-tolerant yield (DTY) QTLs (qDTY1.2, qDTY3.2, qDTY6.1), one heat-tolerance (HT) QTL (qSSPF10) and four yield QTLs (qFLW4.1, qFLL9, LP1, GW5); PL476 with two WUE QTLs (%N11.1, qWue7a), two DTY QTLs (qDTY6.1, qDTY12.1), two HT QTLs (qSSPF10, qHT6) and three yield QTLs (qFLW4.1, qFLL9, LP1); and PL130 with two WUE QTLs (Mr19a, qWue7a), four DTY QTLs (qDTY1.2, qDTY3.2, qDTY4.1, qDTY12.1), two HT QTLs (qSSPF10, qHT6) and two yield QTLs (qFLW4.1, LP1). These three lines shown a yield advantage of 51.93%, 55.93% and 60.30%, respectively, over high-yielding IR64. Under heat stress, PL457 and PL130 with HT QTLs qSSPF10 and qHT6 showed 85.02% and 61.55% yield advantage, respectively, over IR64. In conclusion, we have demonstrated that the systematic combination of important QTLs from two contrasting parents through marker-assisted pedigree breeding is an outstanding approach to supplement conventional phenotype-based pedigree breeding, especially to improve complex traits such as yield and tolerance to moisture stress and heat.

Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

AbstractSubmerged germination ability is a key trait of rice (Oryza sativa L.) in the success of water direct seeding. Therefore, mining submerged germination‐related loci and seeking high tolerant rice germplasms are important for developing rice direct seeding breeding strategies. Here, we treated 272 recombinant inbred lines (RILs, F15) from a cross from Luohui 9 (indica) and RPY geng (japonica) with simulated submergence for 7 days. We successfully bred several superior homozygous RILs with high submergence resistance, namely, R53, R137, R148, R176, and R180, via indica and japonica hybridization strategies. Then, the QTL mapping of coleoptile length trait was performed by R/qtl and IciMapping softwares based on the high‐density bin marker genetic map and two QTLs responsible for coleoptile length were detected in chromosomes 1 (qCL‐1.1) and 3 (qCL‐3.1). The haplotype results of RILs showed that the aggregation of elite alleles of these two QTLs in an individual was beneficial to improving the rice submergence tolerance. According to contrasting genotype of qCL‐1.1 and qCL‐3.1 with different coleoptile lengths, RIL07 (R07) and R180 were selected to further RNA‐seq analysis for analyzing the possible molecular mechanisms of rice under submergence stress. Finally, LOC_Os01g04430, LOC_Os01g04530, and LOC_Os03g22720 for qCL‐1.1 and qCL‐3.1 were characterized to affect submergence stress by the overlapped analysis of two independent sets of RNA‐seq data, qRT‐PCR verification, and gene sequence alignments. In this study, the submerged germination‐related QTLs/genes and high submergence‐tolerant RILs provided new genetic resources for breeding rice varieties suitable for direct seeding via molecular breeding strategies in the immediate future.

Systems genetics analysis of oral squamous cell carcinoma susceptibility using the mouse model: current position and new perspective.

Oral squamous cell carcinoma (OSCC) is one of the most common human malignancies with complex etiology and poor prognosis. Although environmental carcinogens and carcinogenic viruses are still considered the main etiologic factors for OSCC development, genetic factors obviously play a key role in the initiation and progression of this neoplasm, given that not all individuals exposed to carcinogens develop the same severity of the disease, if any. Identifying genetic loci modulating OSCC risk may have several important clinical implications, including early detection, prevention and developing new treatment strategies. Due to limitations in controlled and standardized genetic studies in humans, genetic components underlying susceptibility of OSCC development remain largely unknown. A combination of quantitative trait loci mapping in mice, with complementary association studies in humans, has the potential to discover novel cancer risk loci. As of today, a limited number of genetic analyses were applied on rodent models to locate novel genetic loci associated with human OSCC. Here, we discuss the current status of the mouse models use for dissecting the genetic basis of OSCC and highlight how systems genetics analysis using mouse models, may increase our understanding of human OSCC susceptibility.

Identification of Novel Genomic Regions for Biofortification Traits Using an SNP Marker-Enriched Linkage Map in Wheat (Triticum aestivum L.).

Micronutrient and protein malnutrition is recognized among the major global health issues. Genetic biofortification is a cost-effective and sustainable strategy to tackle malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC), and thousand kernel weight (TKW) were investigated in a set of 163 recombinant inbred lines (RILs) derived from a cross between cultivated wheat variety WH542 and a synthetic derivative (Triticum dicoccon PI94624/Aegilops tauschii [409]//BCN). The RIL population was genotyped using 100 simple-sequence repeat (SSR) and 736 single nucleotide polymorphism (SNP) markers and phenotyped in six environments. The constructed genetic map had a total genetic length of 7,057 cM. A total of 21 novel quantitative trait loci (QTL) were identified in 13 chromosomes representing all three genomes of wheat. The trait-wise highest number of QTL was identified for GPC (10 QTL), followed by GZnC (six QTL), GFeC (three QTL), and TKW (two QTL). Four novel stable QTL (QGFe.iari-7D.1, QGFe.iari-7D.2, QGPC.iari-7D.2, and QTkw.iari-7D) were identified in two or more environments. Two novel pleiotropic genomic regions falling between Xgwm350–AX-94958668 and Xwmc550–Xgwm350 in chromosome 7D harboring co-localized QTL governing two or more traits were also identified. The identified novel QTL, particularly stable and co-localized QTL, will be validated to estimate their effects on different genetic backgrounds for subsequent use in marker-assisted selection (MAS). Best QTL combinations were identified by the estimation of additive effects of the stable QTL for GFeC, GZnC, and GPC. A total of 11 RILs (eight for GZnC and three for GPC) having favorable QTL combinations identified in this study can be used as potential donors to develop bread wheat varieties with enhanced micronutrients and protein.

Identification of Genetic Loci and Candidate Genes Related to Grain Zinc and Iron Concentration Using a Zinc-Enriched Wheat 'Zinc-Shakti'.

The development of nutritionally enhanced wheat (Triticum aestivum L.) with higher levels of grain iron (Fe) and zinc (Zn) offers a sustainable solution to micronutrient deficiency among resource-poor wheat consumers. One hundred and ninety recombinant inbred lines (RILs) from ‘Kachu’ × ‘Zinc-Shakti’ cross were phenotyped for grain Fe and Zn concentrations and phenological and agronomically important traits at Ciudad Obregon, Mexico in the 2017–2018, 2018–2019, and 2019–2020 growing seasons and Diversity Arrays Technology (DArT) molecular marker data were used to determine genomic regions controlling grain micronutrients and agronomic traits. We identified seven new pleiotropic quantitative trait loci (QTL) for grain Zn and Fe on chromosomes 1B, 1D, 2B, 6A, and 7D. The stable pleiotropic QTL identified have expanded the diversity of QTL that could be used in breeding for wheat biofortification. Nine RILs with the best combination of pleiotropic QTL for Zn and Fe have been identified to be used in future crossing programs and to be screened in elite yield trials before releasing as biofortified varieties. In silico analysis revealed several candidate genes underlying QTL, including those belonging to the families of the transporters and kinases known to transport small peptides and minerals (thus assisting mineral uptake) and catalyzing phosphorylation processes, respectively.

Characterizing the Genetic Architecture of Nonhost Resistance in Barley Using Pathogenically Diverse Puccinia Isolates

Barley is an intermediate or near nonhost to many cereal rust pathogens that infect grasses, making it a highly suitable model to understand the evolution and genetic basis of nonhost resistance (NHR) in plants. To characterize the genetic architecture of NHR in barley, we used the Oregon Wolfe Barley doubled haploid and Morex × SusPtrit recombinant inbred line mapping populations. To elicit a wide array of NHR responses, we tested 492 barley accessions and both mapping populations with pathogenically diverse cereal rust isolates representing distinct formae speciales adapted to Avena, Hordeum, Triticum, and Lolium spp.: P. coronata f. sp. avenae (oat crown rust pathogen) and P. coronata f. sp. lolii (ryegrass crown rust pathogen), P. graminis f. sp. avenae (oat stem rust pathogen) and P. graminis f. sp. lolii (the ryegrass stem rust pathogen), and P. striiformis f. sp. tritici (wheat stripe rust pathogen) and P. striiformis f. sp. pseudo-hordei (barley grass stripe rust pathogen). With the exception of P. coronata f. sp. lolii and P. coronata f. sp. avenae, susceptibility and segregation for NHR was observed in the barley accessions and both mapping populations. Quantitative trait loci (QTLs) for NHR were mapped on all seven chromosomes. NHR in barley to the heterologous rusts tested was attributable to a combination of QTLs with either or both overlapping and distinct specificities. Across both mapping populations, broadly effective NHR loci were also identified that likely play a role in host specialization.

Aggressiveness of Diverse French Aphanomyces euteiches Isolates on Pea Near Isogenic Lines Differing in Resistance Quantitative Trait Loci.

Aphanomyces root rot is a major disease in many pea growing regions worldwide. Development of resistant varieties is necessary to manage the disease. Near isogenic lines (NILs) carrying resistance alleles at main quantitative trait loci (QTLs) were developed by marker-assisted backcrossing. This study aimed to evaluate the aggressiveness of diverse French isolates of Aphanomyces euteiches on NILs carrying different resistance QTLs. Forty-three A. euteiches isolates from different French pea growing regions were tested for aggressiveness on eight NILs carrying single or combinations of resistance QTLs and two susceptible or resistant control lines, in controlled conditions. Three clusters of isolates, unrelated to geographical origin, were identified, including 37, 56, and 7% of isolates with high, moderate, and low average levels of aggressiveness, respectively. Three groups of pea lines were also identified. The first group consisted of a pea resistant control line, moderately to highly resistant to all of the isolates. The second group included five NILs carrying a major-effect resistance allele at QTL Ae-Ps7.6, with a medium to broad range of effects on the isolates. The third group consisted of three NILs carrying minor-effect resistance alleles, with a narrow range of effects on the isolates. The results suggest that highly aggressive isolates occur naturally, which may be selected by future partially resistant pea varieties carrying QTLs and increase the risk of erosion of QTL effect. QTL pyramiding strategies for a higher level and a broader range of effect of quantitative resistance on A. euteiches populations will be required for breeding for durable pea resistant varieties.

Grain Inorganic Arsenic Content in Rice Managed Through Targeted Introgressions and Irrigation Management.

Arsenic (As) accumulation in rice grain is a significant public health concern. Inorganic As (iAs) is of particular concern because it has increased toxicity as compared to organic As. Irrigation management practices, such as alternate wetting and drying (AWD), as well as genotypic differences between cultivars, have been shown to influence As accumulation in rice grain. A 2 year field study using a Lemont × TeQing backcross introgression line (TIL) mapping population examined the impact of genotype and AWD severity on iAs grain concentrations. The “Safe”-AWD [35–40% soil volumetric water content (VWC)] treatment did not reduce grain iAs levels, whereas the more severe AWD30 (25–30% VWC) consistently reduced iAs concentrations across all genotypes. The TILs displayed a range of iAs concentrations by genotype, from less than 10 to up to 46 μg kg–1 under AWD30 and from 28 to 104 μg kg–1 under Safe-AWD. TIL grain iAs concentrations for flood treatments across both years ranged from 26 to 127 μg kg–1. Additionally, seven quantitative trait loci (QTLs) were identified in the mapping population associated with grain iAs. A subset of eight TILs and their parents were grown to confirm field-identified grain iAs QTLs in a controlled greenhouse environment. Greenhouse results confirmed the genotypic grain iAs patterns observed in the field; however, iAs concentrations were higher under greenhouse conditions as compared to the field. In the greenhouse, the number of days under AWD was negatively correlated with grain iAs concentrations. Thus, longer drying periods to meet the same soil VWC resulted in lower grain iAs levels. Both the number and combinations of iAs-affecting QTLs significantly impacted grain iAs concentrations. Therefore, identifying more grain iAs-affecting QTLs could be important to inform future breeding efforts for low iAs rice varieties. Our study suggests that coupling AWD practices targeting a soil VWC of less than or equal to 30% coupled with the use of cultivars developed to possess multiple QTLs that negatively regulate grain iAs concentrations will be helpful in mitigating exposure of iAs from rice consumption.

Genome‐wide association reveals limited benefits of pyramiding the 1B and 1D loci with the 2NvS translocation for wheat blast control

AbstractResistance to wheat spike blast (WSB), caused by the Magnaporthe oryzae triticum pathotype (MoT), has relied upon a single major source: the 2NvS translocation introgressed from the wild relative Aegilops ventricosa Tausch. However, this resistance is partial and recently partially overcome by newer MoT races. To characterize potential novel loci conferring resistance to WSB, we conducted a genome‐wide association study (GWAS) using a diverse panel of 384 wheat genotypes phenotyped under three controlled‐environment conditions using MoT isolates T‐25 (301 genotypes), B‐71 (87 genotypes), and 008 (49 genotypes). Genotyping‐by‐sequencing identified 13,175 single nucleotide polymorphisms (SNPs) after filtering. Principal components analysis (PCA) identified two clusters based on the presence or absence of the 2NvS translocation, and the first three PCAs explained 13% of the genetic variation. Three individual analyses were performed (full [all genotypes combined], 2NvS genotypes only, and non‐2NvS genotypes only) using a linear mixed model and a threshold of significance of false discovery rate at 5%. Association analysis detected 25 significant SNPs for the full GWAS with isolate T‐25, in which 21 were mapped on chromosome 2A in the same physical position as the 2NvS translocation. Highly significant linkage disequilibrium among these SNPs suggested they might tag the same quantitative trait locus (QTL). No significant associations were identified with isolates B‐71 and 008, likely due to the small sample size. A QTL pyramiding analysis showed that the combination of multiple QTL was not statistically different from the individual effect of the 2A QTL. Further validation of these genomic regions can aid breeding for broad spectrum and durable WSB resistance.

Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation.

A range of heavy metals are required for normal cell function and homeostasis. However, the anthropogenic release of metal compounds into soil and water sources presents a pervasive health threat. Copper is one of many heavy metals that negatively impacts diverse organisms at a global scale. Using a combination of quantitative trait locus (QTL) mapping and RNA sequencing in the Drosophila Synthetic Population Resource, we demonstrate that resistance to the toxic effects of ingested copper in D. melanogaster is genetically complex and influenced by allelic and expression variation at multiple loci. QTL mapping identified several QTL that account for a substantial fraction of heritability. Additionally, we find that copper resistance is impacted by variation in behavioral avoidance of copper and may be subject to life-stage specific regulation. Gene expression analysis further demonstrated that resistant and sensitive strains are characterized by unique expression patterns. Several of the candidate genes identified via QTL mapping and RNAseq have known copper-specific functions (e.g., Ccs, Sod3, CG11825), and others are involved in the regulation of other heavy metals (e.g., Catsup, whd). We validated several of these candidate genes with RNAi suggesting they contribute to variation in adult copper resistance. Our study illuminates the interconnected roles that allelic and expression variation, organism life stage, and behavior play in copper resistance, allowing a deeper understanding of the diverse mechanisms through which metal pollution can negatively impact organisms.

Effects of combining Renlon with Renbarb1 and Renbarb2 on resistance of cotton (Gossypium hirsutum L.) to reniform nematode (Rotylenchulus reniformis Linford and Oliveria)

The upland cotton (Gossypium hirsutum L.) germplasm lines BARBREN-713, having the Renbarb1 and Renbarb2 quantitative trait loci (QTL), and LONREN, carrying the Renlon QTL, have introgressed resistance to reniform nematode (Rotylenchulus reniformis Linford and Oliveria). Stunting has been observed in the LONREN source of resistance when subjected to heavy nematode pressure but not for BARBREN-713. To investigate the potential to reduce stunting in the LONREN source of resistance, cotton lines were developed with different combinations of reniform nematode resistance QTL from LONREN and BARBREN-713. Marker assisted selection was conducted to identify the following QTL combinations: (1) Renbarb1 + Renbarb2, (2) Renbarb1 + Renbarb2 + Renlon, (3) Renbarb2 + Renlon, (4) Renbarb1 + Renlon, (5) Renbarb1 alone, (6) Renbarb2 alone, (7) Renlon alone, and (8) a Null susceptible genotype. QTL combinations were inoculated with 0, 2300, or 5000 reniform nematodes per 120 cm3 soil in growth chamber tests. Plants were harvested at 60 days after inoculation, plant growth measurements made, and the nematode reproduction factor calculated. In this study, the Renbarb1 genotype was scored as susceptible to reniform nematode. Combining Renlon with Renbarb2 did not improve resistance to reniform nematode; however, the Renbarb2/Renlon combination showed improved growth compared to LONREN-1, BARBREN-713, and the susceptible null check.

Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure.

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co-localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked-down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.

Genome-wide association mapping of QTLs implied inpotato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.

SummaryIn this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping‐by‐sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome‐wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.

Identification of Quantitative Trait Loci for the Concentrations of Phenylpropanoid Glycosides in Brown Rice.

Rice (Oryza sativa L.) is a staple food for most of the world’s population, as it is eaten by nearly half of its inhabitants. Phenylpropanoid glycosides derived from plants have various biomedical effects. The comparison of the concentrations of the four major phenylpropanoid glycosides in brown rice, i.e., 6-O-feruloylsucrose (1), 3′,6-di-O-sinapoylsucrose (2), 3′-O-sinapoyl-6-O-feruloylsucrose (3), and 3′,6-di-O-feruloylsucrose (4), between a conventional japonica-type cultivar Koshihikari and a high-yielding indica-type cultivar Takanari revealed that they were 57–162% higher in Koshihikari than in Takanari. To identify quantitative trait loci (QTLs) for the concentrations of these compounds (1–4), reciprocal chromosome segment substitution lines derived from a cross between Koshihikari and Takanari were analyzed. We identified QTLs for the concentrations of compound 1 on chromosome 2 and of compound 2 on chromosome 4 in the reciprocal genetic background. The concentrations of these compounds were increased by the Koshihikari alleles and decreased by the Takanari alleles. Therefore, the favorable alleles of Koshihikari are available to ameliorate the lower concentrations of compounds 1 and 2 in Takanari. The combinations of QTLs identified in the present study together with those of other biologically active compounds make it possible to breed health beneficial cultivars.

Identification of quantitative trait loci for panicle structure and grain filling using a cross between indica- and japonica-type high-yielding rice cultivars

ABSTRACTTo enhance the yield potential of rice by breeding, it is important to reveal the genetic factors affecting yield components in high-yielding cultivars. Quantitative trait loci (QTL) analysis for panicle structure and spikelet weight as an index of grain filling was conducted using recombinant inbred lines (RILs) derived from a cross between an indica-dominant high-yielding cultivar, Takanari, and a japonica-dominant high-yielding cultivar, Momiroman in 2012 and 2013 in eastern Japan. The grain-filling ability of Takanari is reported to be better than that of Momiroman. Since grain filling is generally better near the tip of the panicle and decreases as the number of branches from the rachis increases, we classified whole panicles into upper and lower side panicles and spikelets into primary, secondary, and tertiary spikelets according to the number of branches from the rachis. On chromosomes 1, 4, and 6, QTLs regulating the number of spikelets per panicle and panicle structure were detected and were most likely identical to GN1a, SPIKE, and APO1, respectively, which has been previously reported as QTLs regulating the number of spikelets per panicle. Takanari produced much heavier secondary and tertiary spikelets than Momiroman on the lower side panicle. On chromosome 5, novel QTLs regulating spikelet weight were detected. The Takanari allele enhanced secondary and tertiary spikelet weight on the lower side panicle. These results indicate that it may be possible to enhance sink capacity and translocation of source with a combination of novel QTLs detected on chromosome 5 and GN1, APO1, and SPIKE.