Identification Of QTL Research Articles

Identification and validation of a major QTL controlling the presence/absence of leaf lobes in Brassica rapa L.

Leaves are vital plant organs, and a high level of variation in leaf shape, including the leaf lobes, is present in Brassica rapa. Based on a previously-constructed linkage map, QTL analysis of the leaf lobes was performed using the scores from an F2 population during the spring of 2010, and scores from an F2:3 family in the autumn of 2010, respectively. A total of nine QTLs were found to affect leaf lobes. Among these, a major QTL, lob 10.1, was mapped to the bottom of linkage group A10. To develop near iso-genic lines (NILs) for the identified major QTL, an F2 plant without leaf lobes that was homozygous in the targeted region for marker alleles from the male parent (08A061), was backcrossed to 09A001, the recurrent parent with leaf lobes. Two InDel marker loci, BrID10909 and BrID10233, which are closely linked to the major QTL peak position, and 166 SSR and InDel markers from non-targeted chromosomal regions, were used for foreground and background selection, respectively. Three sets of NILs were developed through four cycles of backcrossing followed by two cycles of self-pollination. Compared to 09A001, the recurrent parent, all the NILs showed the absence of leaf lobes and had no significant differences in other agriculturally important traits. NILs are the ideal genetic resource for QTL validation and fine-scale linkage mapping, and, ultimately, gene discovery.

Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6cM and had an average of one marker every 1.26cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.

QTL identification on two genetic systems for rapeseed glucosinolate and erucic acid contents over two seasons

Glucosinolate and erucic acid are important plant compounds in rapeseed believed to have numerous functions in rapeseed-environment interactions. However, little is known about the QTL information related to the two different genetic systems including the embryo nuclear chromosomes and maternal plant nuclear chromosomes for glucosinolate content (GSLC) and erucic acid content (EAC) in rapeseed. Differences in QTL distribution between these two genetic systems, which control the performance of GSLC and EAC across different environmental conditions, were analyzed in the present study. A set of 202 DH populations derived from an elite hybrid cross of ‘Tapidor’ × ‘Ningyou7’ and their two backcross populations BC1F1 1 (DHs × Tapidor) and BC1F1 2 (DHs × Ningyou7) generated in two years were used as experimental materials for the study. A total of nine loci for GSLC and three loci for EAC with significant embryo additive main effects, embryo dominant main effects and/or maternal additive main effects, explaining 83.8 and 89.7 %, respectively, of their phenotypic variation, were identified. Although QTL × environment interaction effects were also detected in the present experiment, they played a minimum role in influencing the phenotypic variation. It was noted that qEAC-7-1 for EAC mapped on linkage group A7 was detected as the major QTL and could explain 68.32 % of the phenotypic variation for this trait. These results could be useful for the molecular maker-assisted breeding of GSLC and EAC quality traits based on the influence of two genetic systems.

Identification of QTL for leaf angle and leaf space above ear position across different environments and generations in maize (Zea mays L.)

The yield of maize (Zea mays L.) is affected by the plant architecture which is associated with the distribution of light within canopy and utilization of solar energy within population. Plant architecture of maize is mainly characterized by leaf angle (LA) and leaf space (LS). To analyze the genetic mechanism of LA and LS above ear position in maize, a genetic linkage map composed of 212 simple sequence repeat markers was constructed based on a F2 population derived from the cross between the compact inbred line CY5 and the expanded inbred line YL106. The map spanned 1,153.39 cM in length with an average interval of 5.44 cM. By using the inclusive composite interval mapping method, QTLs for LA and LS above ear position were identified based on two field mapping populations consisted of 144 F2:3 families in three environments and 144 F4 families, respectively. In F2:3 population, three consistent QTLs qSecLA1a, qThiLA1a, and qThiLS7 were detected in both single-environment analysis and joint-environment analysis. The qSecLA1a between bnlg1803 and bnlg1007 on chromosome 1.02 explained 26.99 and 18.51 % of the phenotypic variation, qThiLA1a between bnlg1803 and bnlg1007 on chromosome 1.02 explained 24.14 and 22.00 % of the phenotypic variation and qThiLS7 between bnlg1305 and umc1787 on chromosome 7.02/7.03 explained 13.77 and 9.96 % of the phenotypic variation in single environment analysis while the three QTLs explained 29.10, 31.86 and 11.20 % of the phenotypic variation, respectively in joint environment analysis. Moreover, there were major QTLs near bnlg1803 on chromosome 1 for SecLA and ThiLA stably expressing in F2:3 and F4 generations. The results of this study could provide references for genetic modification and molecular marker-assisted selection for LA and LS in maize.

A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.)

We used RAD (restriction-site-associated DNA) sequencing to detect genome-wide SNPs and construct a dense linkage map using an intercross F2 population in jute (Corchorus olitorius). The linkage map comprising a total of 503 RAD markers in seven linkage groups spanned 358.5 cM with an average marker interval of 0.72 cM and covered 87.0 % of the genome. Genome-wide segregation distortion of the mapped loci (34.4 %) was non-random across the linkage map, with a directional bias mostly towards the female genotypes. Jute had maximum syntenic relationships with cocoa (47.5 % homology) and diploid cotton (29.2 % homology). However, synteny and collinearity were not conserved. Histological fibre content (FC; total number of fibre cell bundles in a stem cross section) was positively correlated with fibre yield (FY), plant height (PH), root weight (RW) and stem-base diameter (SBD). Broad-sense heritability estimates were high for all traits, with FC and FY showing maximum heritability (~93 %). QTL mapping based on the F2:3 phenotypes detected nine QTL across the two environments. The QTL for FC was coincident with one QTL each for FY, PH, RW and SBD on top of a single-SNP (C/T) marker at 40.2 cM on LG1, each accounting for ~7–11 % of the phenotypic variance. Two QTL linked in repulsion one each for PH and SBD, with varying degrees of overdominance, were associated with two single-SNP (C/T) markers on LG2, each accounting for ~17–18 % of the phenotypic variance. Few candidate genes were identified within the QTL regions. Our results would enable development of tools for marker-assisted selection in jute.

Identification of QTL Associated with Vitamin E Content in Soybean Seeds

Identification of QTL Associated with Vitamin E Content in Soybean Seeds

Identification of QTL for crop timing and quality traits in an interspecific Petunia population

Genetic mapping in ornamental plant species has lagged behind crop plants from other sectors of agriculture. Here, we describe the generation of a genetic linkage map for the important herbaceous ornamental crop petunia and the identification of QTL for several key crop timing and quality traits, including plant development rate, days to flower and flower number. An F2 population derived from a cross between the progenitor species of cultivated petunia, P. integrifolia × P. axillaris, exhibited transgressive segregation for a broad panel of crop timing and quality traits. A genetic linkage map comprised of 75 simple sequence repeat and six cleaved amplified polymorphic sequence markers spanning 359.1 cM across seven linkage groups was developed and utilized to identify 24 QTL for ten crop timing and quality traits. These included QTL explaining 26.3, 25.9, 26.2 and 43 % of the observed phenotypic variation for flower length, branch number, internode length and the number of flower buds on the primary shoot, respectively. These data provide a foundation for understanding the genetic control of critical traits and identify molecular markers with potential utility to facilitate gene discovery in petunia.

The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.

Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ∼100% and ∼33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ∼6×10−5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio.

Bioinformatics: identification of markers from next-generation sequence data.

With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

The genetic basis of variation in clean lineages of Saccharomyces cerevisiae in response to stresses encountered during bioethanol fermentations.

Saccharomyces cerevisiae is the micro-organism of choice for the conversion of monomeric sugars into bioethanol. Industrial bioethanol fermentations are intrinsically stressful environments for yeast and the adaptive protective response varies between strain backgrounds. With the aim of identifying quantitative trait loci (QTL's) that regulate phenotypic variation, linkage analysis on six F1 crosses from four highly divergent clean lineages of S. cerevisiae was performed. Segregants from each cross were assessed for tolerance to a range of stresses encountered during industrial bioethanol fermentations. Tolerance levels within populations of F1 segregants to stress conditions differed and displayed transgressive variation. Linkage analysis resulted in the identification of QTL's for tolerance to weak acid and osmotic stress. We tested candidate genes within loci identified by QTL using reciprocal hemizygosity analysis to ascertain their contribution to the observed phenotypic variation; this approach validated a gene (COX20) for weak acid stress and a gene (RCK2) for osmotic stress. Hemizygous transformants with a sensitive phenotype carried a COX20 allele from a weak acid sensitive parent with an alteration in its protein coding compared with other S. cerevisiae strains. RCK2 alleles reveal peptide differences between parental strains and the importance of these changes is currently being ascertained.

Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

QTLs for quantitative traits are influenced by genetic background (GB) and environment. Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection (MAS). In this study, QTLs and QTL×environment interactions affecting grain yield per plant (GY) and its component traits, filled grain number per panicle (FGN), panicle number per plant (PN) and 1000-grain weight (TGW) across six environments were dissected using two sets of reciprocal introgression lines (ILs) derived from the cross Lemont×Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs (87.4%) showed significant QTL×environment interactions (QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15 (20.8%) QTLs and 12 (16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

Identification of QTL for adult-plant resistance to powdery mildew in Chinese wheat landrace Pingyuan 50

Powdery mildew caused by Blumeria graminis f. sp. tritici is one of the major wheat diseases worldwide. The Chinese wheat landrace Pingyuan 50 has shown adult-plant resistance (APR) to powdery mildew in the field for over 60years. To dissect the genetic basis of APR to powdery mildew in this cultivar, a mapping population of 137 double haploid (DH) lines derived from Pingyuan 50/Mingxian 169 was evaluated in replicated field trials for two years in Beijing (2009–2010 and 2010–2011) and one year in Anyang (2009–2010). A total of 540 polymorphic SSR markers were genotyped on the entire population for construction of a linkage map and QTL analysis. Three QTL were mapped on chromosomes 2BS (QPm.caas-2BS.2), 3BS (QPm.caas-3BS), and 5AL (QPm.caas-5AL) with the resistance alleles contributed by Pingyuan 50 explaining 5.3%, 10.2%, and 9.1% of the phenotypic variances, respectively, and one QTL on chromosome 3BL (QPm.caas-3BL) derived from Mingxian 169 accounting for 18.1% of the phenotypic variance. QPm.caas-3BS, QPm.caas-3BL, and QPm.caas-5AL appear to be new powdery mildew APR loci. QPm.caas-2BS.2 and QPm.caas-5AL are possibly pleiotropic or closely linked resistance loci to stripe rust resistance QTL. Pingyuan 50 could be a potential genetic resource to facilitate breeding for improved APR to both powdery mildew and stripe rust.

Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress

BackgroundDrought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought.ResultsQTL analysis revealed major-effect GY QTL: qDTY 1.2 , qDTY 2.2 and qDTY 1.3 , qDTY 2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY 1.2 and qDTY 2.2 explained an additive effect of 288 kg ha−1 and 567 kg ha−1 in Kali Aus/2*MTU1010, whereas qDTY 1.3 and qDTY 2.3 explained an additive effect of 198 kg ha−1 and 147 kg ha−1 in Kali Aus/2*IR64 populations, respectively.Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154–RM324 and RM263–RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488–RM315 and chromosome 2 at RM324–RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations.ConclusionThe QTL, qDTY 1.2 , qDTY 1.3 , qDTY 2.2 , and qDTY 2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield under drought. The observed epistatic interaction for GY and DTF will contribute to our understanding of the genetic basis of agronomically important traits and enhance predictive ability at an individualized level in agriculture.

Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response.

Hevea brasiliensis is a native species of the Amazon Basin of South America and the primary source of natural rubber worldwide. Due to the occurrence of South American Leaf Blight disease in this area, rubber plantations have been extended to suboptimal regions. Rubber tree breeding is time-consuming and expensive, but molecular markers can serve as a tool for early evaluation, thus reducing time and costs. In this work, we constructed six different cDNA libraries with the aim of developing gene-targeted molecular markers for the rubber tree. A total of 8,263 reads were assembled, generating 5,025 unigenes that were analyzed; 912 expressed sequence tags (ESTs) represented new transcripts, and two sequences were highly up-regulated by cold stress. These unigenes were scanned for microsatellite (SSR) regions and single nucleotide polymorphisms (SNPs). In total, 169 novel EST-SSR markers were developed; 138 loci were polymorphic in the rubber tree, and 98 % presented transferability to six other Hevea species. Locus duplication was observed in H. brasiliensis and other species. Additionally, 43 SNP markers in 13 sequences that showed similarity to proteins involved in stress response, latex biosynthesis and developmental processes were characterized. cDNA libraries are a rich source of SSR and SNP markers and enable the identification of new transcripts. The new markers developed here will be a valuable resource for linkage mapping, QTL identification and other studies in the rubber tree and can also be used to evaluate the genetic variability of other Hevea species, which are valuable assets in rubber tree breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0095-2) contains supplementary material, which is available to authorized users.

Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci

BackgroundThe identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data.ResultsFor the identification of genes underlying known heterotic QTL, we made use of tight associations between gene expression pattern and the trait of interest, identified by correlation analyses. Using this approach genes strongly associated with heterosis for GY were discovered to be clustered in pericentromeric regions of the complex maize genome. This suggests that expression differences of sequences in recombination-suppressed regions are important in the establishment of heterosis for GY in F1 hybrids and also in the conservation of heterosis for GY across genotypes. Importantly functional analysis of heterosis-associated genes from these genomic regions revealed over-representation of a number of functional classes, identifying key processes contributing to heterosis for GY. Based on the finding that the majority of the analyzed heterosis-associated genes were addtitively expressed, we propose a model referring to the influence of cis-regulatory variation on heterosis for GY by the compensation of fixed detrimental expression levels in parents.ConclusionsThe study highlights the utility of a meta-analysis approach that integrates phenotypic and multi-level molecular data to unravel complex traits in plants. It provides prospects for the identification of genes relevant for QTL, and also suggests a model for the potential role of additive expression in the formation and conservation of heterosis for GY via dominant, multigenic quantitative trait loci. Our findings contribute to a deeper understanding of the multifactorial phenomenon of heterosis, and thus to the breeding of new high yielding varieties.

Identification of Major and Minor QTL for Ecologically Important Morphological Traits in Three-Spined Sticklebacks (Gasterosteus aculeatus)

Quantitative trait locus (QTL) mapping studies of Pacific three-spined sticklebacks (Gasterosteus aculeatus) have uncovered several genomic regions controlling variability in different morphological traits, but QTL studies of Atlantic sticklebacks are lacking. We mapped QTL for 40 morphological traits, including body size, body shape, and body armor, in a F2 full-sib cross between northern European marine and freshwater three-spined sticklebacks. A total of 52 significant QTL were identified at the 5% genome-wide level. One major QTL explaining 74.4% of the total variance in lateral plate number was detected on LG4, whereas several major QTL for centroid size (a proxy for body size), and the lengths of two dorsal spines, pelvic spine, and pelvic girdle were mapped on LG21 with the explained variance ranging from 27.9% to 57.6%. Major QTL for landmark coordinates defining body shape variation also were identified on LG21, with each explaining ≥15% of variance in body shape. Multiple QTL for different traits mapped on LG21 overlapped each other, implying pleiotropy and/or tight linkage. Thus, apart from providing confirmatory data to support conclusions born out of earlier QTL studies of Pacific sticklebacks, this study also describes several novel QTL of both major and smaller effect for ecologically important traits. The finding that many major QTL mapped on LG21 suggests that this linkage group might be a hotspot for genetic determinants of ecologically important morphological traits in three-spined sticklebacks.

Applications of genomics to improve livestock in the developing world

Nearly 25 years have passed since much of the original molecular genetics research began in livestock. Since then activities in the livestock community have been associated with gene identification, gene mapping, QTL identification, genome-wide association studies and more recently the completion of initial sequencing of all the major livestock species. Many individual genes have been identified and incorporated into selection schemes in livestock, and more recently whole genome analysis and genomic selection have begun to be applied. The advent of cheaper, faster sequencing technologies and the realization of good draft sequences and development of SNP chip technologies for livestock species have contributed to our understanding on many ways to further improve our important food species. Such discoveries generally have benefitted three groups: livestock producers, consumers in the developed world and biomedical researchers. However, increased food insecurity and a worldwide food production crisis loom in the future as the most significant scientific challenge facing us in the next 30 years. Expectations are that human population growth will soon go from 7.3 billion to 9.6 billion by 2050, and food production must double despite evidence of climate change and limited land and water resources. There is a significant increased demand for animal source foods especially in the poorer countries of the developing world where most livestock are produced by small holders but also in countries like China and Brazil which are transforming quickly. Many researchers have touted that the genomic revolution offers solutions to increasing food in the developing world. These opportunities certainly exist, from identifying signatures of selection associated with adaptations for these environments to reducing susceptibility to major disease agents. Direction and focus of research, funding issues and human capacity training all will be required for success. Genomic discoveries will need to be embedded within sustainable programs that address implementation from the outset, and benefiting small holder production will be crucial to meeting this challenge.

Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities.

BackgroundAvailability of irrigation water is becoming a major limiting factor in rice cultivation. Production in rainfed areas is affected in particular by drought events, as these areas are commonly planted to high-yielding drought-susceptible rice (Oryza sativa L.) varieties. The use of bulk segregant analysis (BSA), taking grain yield (GY) as a selection criterion, has resulted in the identification of several large-effect QTL. A QTL mapping study was undertaken on a BC1F3:4 population developed from the cross IR55419-04/2*TDK1 with the aim of identifying large-effect QTL in the background of TDK1, a popular variety from Lao PDR.ResultsThe study identified three QTL—qDTY 3.1 (RM168-RM468), qDTY 6.1 (RM586-RM217), and qDTY 6.2 (RM121-RM541)—for grain yield under drought. qDTY 3.1 and qDTY 6.1 , showed consistent effect across seasons under lowland drought-stress conditions while qDTY 6.1 and qDTY 6.2 showed effect under both upland and lowland drought conditions. The test of QTL effect, conducted through a QTL class analysis, showed the complimentary nature of qDTY 3.1 and qDTY 6.1 . Both QTL showed specific patterns of effect across different maturity groups within the mapping population and higher stability for grain yield was seen across stress levels for lines with both QTLs as compared to those with single or no QTL.ConclusionsThe study offers a clear understanding of large-effect QTL for grain yield under drought and their effect as individual QTL and in various combinations. The study also opens up an opportunity to develop a drought-tolerant version of TDK1 through marker-assisted backcross breeding and has led to a large-scale QTL pyramiding program aiming to combine these QTL with Sub1 in the background of TDK1 as recipient variety.

Genome-wide Identification and Characterization of the Gene Families Controlling Fatty Acid Biosynthesis in Flax (Linum usitatissimum L)

Flax (Linum usitatissimum L.) is an important crop with many characteristic features such as its abundant essential ω-3 fatty acids for human nutrition. Fatty acid (FA) biosynthesis in plants, including flax, involves several consecutive steps governed by different gene families. Using in silico gene mining and comparative analysis, genome-wide gene identification and characterization were performed for six gene families related to FA biosynthesis, including KAS, SAD, FAD, KCS and FAT. We identified 91 FA-related genes from flax cv. CDC Bethune genome, from which seven previously cloned genes were validated. The newly identified 84 FA-related genes include 14 novel genes from the KAS family, two from the SAD family, 13 from the FAD2 family, three from the FAD3 family, 38 from the KCS family and 14 from the FAT family. Out of the 91 genes identified, 88 were duplicated as a consequence of recent whole genome duplication events, in which 13 FAD2 genes were hypothesized to have evolved from tandem gene duplication events followed by a whole genome duplication event and, more recently, by a single gene deletion. The six gene families described here are highly conserved in plants and have diverged anciently. These newly identified flax genes will be a useful resource for further research on FA gene cloning and expression, QTL identification, marker development and marker-assisted selection.