Key Quantitative Trait Loci Research Articles

QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice.

Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F2 population (NIL-13B4 × GH998). Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs) and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2) and LOC_Os06g15420 (asparagine synthetase) were observed between two parents (Y11 and GH998). Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1) and AT5G65010 (ASN2), which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.

Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population.

Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51–7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize.

QTL mapping for haploid male fertility by a segregation distortion method and fine mapping of a key QTL qhmf4 in maize.

Four QTL related to haploid male fertility were detected by a segregation distortion method and the key QTL qhmf4 was fine mapped to an interval of ~800kb. Doubled haploid (DH) technology enables rapid development of homozygous lines in maize breeding programs. However, haploid genome doubling is a bottleneck for the commercialization of DH technology and is limited by haploid male fertility (HMF). This is the first study reporting the quantitative trait locus (QTL) analysis of HMF in maize. Four QTL, qhmf1, qhmf2, qhmf3, and qhmf4, controlling HMF have been identified by segregation distortion (SD) loci detection in the selected haploid population derived from 'Yu87-1/Zheng58'. Three loci, qhmf1, qhmf2, and qhmf4, were also detected in the selected haploid population derived from '4F1/Zheng58'. The QTL qhmf4 showed the strongest SD in both haploid populations. Based on the sequence information of 'Yu87-1' and 'Zheng58', thirteen markers being polymorphic between the two lines were developed to saturate the qhmf4 region. A total of 8168 H1BC2 (haploid backcross generation) plants produced from 'Yu87-1' and 'Zheng58' were screened for recombinants. All the 48 recombinants were backcrossed to 'Zheng58' to develop H1BC3 progeny. The heterozygous H1BC3 individuals were crossed with CAU5 to induce haploids. In each H1BC3 progeny, haploids were genotyped and evaluated for anther emergence score (AES). Significant (or no significant) difference (P < 0.05) between haploids with or without 'Yu87-1' donor segment indicated presence or absence of qhmf4 in the donor segment. The analysis of the 48 recombinants narrowed the qhmf4 locus down to an ~800kb interval flanked by markers IND166 and IND1668.

Genetic interactions improve models of quantitative traits.

A study of genetic variation in yeast has identified key quantitative trait loci (QTLs) that suppress the effects of variation at multiple other loci. These loci prove essential to accurately modeling yeast growth in response to different environments.

How trees allocate carbon for optimal growth: insight from a game-theoretic model.

How trees allocate photosynthetic products to primary height growth and secondary radial growth reflects their capacity to best use environmental resources. Despite substantial efforts to explore tree height-diameter relationship empirically and through theoretical modeling, our understanding of the biological mechanisms that govern this phenomenon is still limited. By thinking of stem woody biomass production as an ecological system of apical and lateral growth components, we implement game theory to model and discern how these two components cooperate symbiotically with each other or compete for resources to determine the size of a tree stem. This resulting allometry game theory is further embedded within a genetic mapping and association paradigm, allowing the genetic loci mediating the carbon allocation of stemwood growth to be characterized and mapped throughout the genome. Allometry game theory was validated by analyzing a mapping data of stem height and diameter growth over perennial seasons in a poplar tree. Several key quantitative trait loci were found to interpret the process and pattern of stemwood growth through regulating the ecological interactions of stem apical and lateral growth. The application of allometry game theory enables the prediction of the situations in which the cooperation, competition or altruism is an optimal decision of a tree to fully use the environmental resources it owns.

Regulation of phosphorus uptake and utilization: transitioning from current knowledge to practical strategies.

Phosphorus is a poorly bioavailable macronutrient that is essential for crop growth and yield. Overuse of phosphorus fertilizers results in low phosphorus use efficiency (PUE), has serious environmental consequences and accelerates the depletion of phosphorus mineral reserves. It has become extremely challenging to improve PUE while preserving global food supplies and maintaining environmental sustainability. Molecular and genetic analyses have revealed the primary mechanisms of phosphorus uptake and utilization and their relationships to phosphorus transporters, regulators, root architecture, metabolic adaptations, quantitative trait loci, hormonal signaling and microRNA. The ability to improve PUE requires a transition from this knowledge of molecular mechanisms and plant architecture to practical strategies. These could include: i) the use of arbuscular mycorrhizal fungal symbioses for efficient phosphorus mining and uptake; ii) intercropping with suitable crop species to achieve phosphorus activation and mobilization in the soil; and iii) tissue-specific overexpression of homologous genes with advantageous agronomic properties for higher PUE along with breeding for phosphorus-efficient varieties and introgression of key quantitative trait loci. More effort is required to further dissect the mechanisms controlling phosphorus uptake and utilization within plants and provide new insight into the means to efficiently improve PUE.

QTL mapping of grain yield and phosphorus efficiency in barley in a Mediterranean-like environment.

Key QTLs were identified for P efficiency in barley. Phosphorus efficiency and grain yield can be improved simultaneously in breeding. An important breeding goal for many crop species is improved phosphorus (P) efficiency. As in many other crops, selection for P efficient barley varieties has been slow because of inconsistent definitions of P efficiency and unknown genetic controls of P efficiency. We used two criteria to assess P efficiency in a doubled haploid Commander/Fleet population: P responsiveness (estimated as the deviation from the regression of yield with added P against yield with no added P treatment) and PUE (relative yield). Phosphorus responsiveness, PUE and grain yield were phenotyped at 0 and 30kgP/ha in five environments. Lines consistently responsive to 30kgP/ha across environments had the highest yield at the two P rates, and P responsiveness showed significantly higher broad sense heritability than PUE in the materials we studied. Genotyping of the population was subjected to a 9,000 single nucleotide polymorphism array and quantitative trait loci (QTLs) for P responsiveness were mapped with yield at 30kgP/ha, which are common QTLs for yield when P was not limiting growth. The largest QTL for P responsiveness was mapped to 7HL in 2years. PUE varied from 31 to 124% across environments and one of the QTLs for PUE was mapped with yield at 0kgP/ha. Our results demonstrate P responsiveness and grain yield can be improved simultaneously under high-input agricultural systems, but breeding for high PUE varieties may need to explore landrace or wild barley germplasm for low P tolerant alleles.

A computational framework for mapping the timing of vegetative phase change.

Phase change plays a prominent role in determining the form of growth and development. Although considerable attention has been focused on identifying the regulatory control mechanisms of phase change, a detailed understanding of the genetic architecture of this phenomenon is still lacking. We address this issue by deriving a computational model. The model is founded on the framework of functional mapping aimed at characterizing the interplay between quantitative trait loci (QTLs) and development through biologically meaningful mathematical equations. A multiphasic growth equationwas implemented into functional mapping, which, via a series of hypothesis tests, allows the quantification of how QTLs regulate the timing and pattern of vegetative phase transition between independently regulated, temporally coordinated processes. The model was applied to analyze stem radial growth data of an interspecific hybrid family derived from two Populus species during the first 24yr of ontogeny. Several key QTLs related to phase change have been characterized, most of which were observed to be in the adjacent regions of candidate genes. The identification of phase transition QTLs, whose expression is regulated by endogenous and environmental signals, may enhance our understanding of the evolution of development in changing environments.

Characterizing Variation of Branch Angle and Genome-Wide Association Mapping in Rapeseed (Brassica napus L.).

Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.

Genetic dissection of leaf-related traits using 156 chromosomal segment substitution lines

A two-line super-hybrid rice (Oryza sativa L.) variety [Liangyoupei9 (LYP9)] demonstrated superiority over its both parents, viz. elite inbred lines 93-11 and Pei-ai64S (PA64S), as well as other conventional hybrids, and had long been exploited in China. However, the genetic basis of its leaf-related traits, supposed to be an important component for yield potential, remains elusive. Here, initially a set of chromosome segment substitution lines (CSSLs) was constructed, in which the genome of Pei-ai64S has been introgressed into the background of 93-11. This set was developed by marker aided selection, based on 123 polymorphic SSR markers. The introgressed chromosomal segments presented in the 156 CSSLs covered 96.46% of Pei-ai64S genome. Afterwards, the CSSLs were deployed to assess the genetic basis of leaf size (length and width) and chlorophyll content of top three leaves across five different environments. The CSSLs showed transgressive segregation for all of the traits, and significant correlations were detected among most of the traits. A total of 27 quantitative trait loci (QTL) were identified on ten chromosomes, and three QTL cluster affecting related traits were found on chromosome 3, 6, and 8, respectively. Remarkably, two key QTLs, qALW3-1 and qALW3-2, both controlling the antepenultimate leaf width, were identified in all five environments, and their effect were further validated by CSSLs harboring the two QTL alleles. Our results indicate that developing CSSLs is a powerful tool for genetic dissection of quantitative traits. Meanwhile, the QTLs controlling leaf-related traits uncovered here provide useful information for marker-assisted selection in improving the performance of leaf morphology and photosynthetic ability.

English

Considerable effort has been made to improve drought-stress tolerance in sorghum by incorporating the stay-green trait into drought-susceptible elite sorghum varieties. Keeping track of the several genes involved in the expression of this complex trait during the breeding program is an enormous task. In this study, the fidelity of recently identified SSR markers were tested for introgression of stay-green QTLs into elite sorghum lines. Of the 102 SSR loci tested, seventy- eight (78) markers were found to be polymorphic between the donor lines (B35 and E36-1) and the recipient lines (Sekedo and Seredo). In total, 25 polymorphisms were detected in SSR loci flanking key stay-green quantitative trait loci (QTLs) from the B35 donor line, and 6 in E36-1. In B35, 5 SSR markers were linked to the QTL StgA, 6 linked to StgB, 3 linked to Stg1, 2 linked to Stg2, 4 linked to Stg3 and 5 linked to Stg4. In contrast, only 6 polymorphic SSR markers were detected in the vicinity of key QTLs found in E36-1. Two were linked to LGA, 1 to LGJ and 3 to LGG. No markers were found linked to QTL LGD and LGH. Similar SSR polymorphisms were observed for markers needed to recover the recurrent parent genomes (RPG) in the subsequent backcross generations. These findings reveal the limitations of using E36-1 as a donor parent in marker-assisted selection (MAS) programmes for improvement of drought tolerance. Low hybridization efficiency (22.5%) was achieved using the anther dehiscence method. Such low hybridization efficiency requires use of molecular markers to easily identify plants harbouring the required genotypes. Key words: Stay-green, drought tolerance, quantitative trait loci (QTL), simple sequence repeat (SSR) markers, polymorphism.

Quantitative trait loci mapping for flag leaf traits in rice using a chromosome segment substitution line population

AbstractTo study the genetic basis of rice flag leaf morphology, quantitative genetic analysis was conducted in a population of 37 chromosome segment substitution lines (CSSLs) of indica elite variety ‘Habataki’ in the background of japonica cultivar ‘Sasanishiki’ across three different environments. The CSSLs showed normal distribution with transgressive segregation, indicating that these four traits are controlled by polygenes. Moreover, analyses of variance showed that these traits were highly influenced by the growing environment, which are typical for polygenic quantitative traits. Seven quantitative trait loci (QTLs) on four chromosomes were detected in total: four for flag leaf width, one for flag leaf area and two for flag leaf angle. Two key QTLs, qFLW4 and qFLAG5 controlling flag leaf width and angle, respectively, were identified in all three environments. These QTLs could provide useful information for marker‐assisted selection in improving the performance of plant architecture with regard to leaf angle and area. Moreover, developed CSSLs with these QTLs information are also useful research materials to reveal the importance of leaf morphology in relation to grain yield.

Correlation analysis and QTL mapping of osmotic potential in japonica rice under upland and lowland conditions

Mu, P. and Li, Z. 2013. Correlation analysis and QTL mapping of osmotic potential in japonica rice under upland and lowland conditions. Can. J. Plant Sci. 93: 785–792. In order to reveal the genetic basis of differences in osmotic potential (OP) of japonica rice under various water regimes, a recombinant inbreed line (RIL) population including 120 plants derived from a cross between an upland japonica rice IRAT109 and a paddy japonica rice Yuefu was used in this study. A complete genetic linkage map with 201 simple sequence repeat (SSR) molecular markers was constructed. Osmotic potentials of the RIL population and their parents were measured pre-dawn and at mid-day under lowland (no soil water stress) and upland (soil water stress) conditions. Significant correlations between osmotic difference (ODl) and (ODu) and index of drought resistance (IDR, based on relative yield in upland and lowland treatments) was found under lowland and upland conditions. Quantitative trait loci (QTL) associated with osmotic potentials and osmotic differences under lowland and upland conditions were detected by using the software QTL MAPPER version 2.0. Twelve additive QTL and 10 pairs of epistatic QTL for OP and OD were detected. Three additive QTL and a pair of epitatic QTL for IDR were also obtained. There were more Q×E QTL and epistatic QTLs under upland conditions than under lowland conditions, indicating that the genetic pattern was more complex under upland conditions than under lowland conditions. Two QTL near RM493–RM1287 on chromosome 1 and RM332–RM1124 on chromosome 11 were found to have a high general contribution of over 10% and may be the key QTL controlling osmotic potential. These results reveal that osmotic potential is a quantitative trait controlled by both additive and epistatic QTL, which are mainly distributed on chromosomes 1, 2, 8 and 9.

A key QTL cluster is conserved among accessions and exhibits broad-spectrum resistance to Phytophthora capsici: a valuable locus for pepper breeding

Developing cultivars carrying effective resistance against destructive pathogens has become a priority for breeders. While little is currently known about the genetic basis of durable resistance, it is generally associated with polygenic and broad-spectrum resistance. In this study, we assessed the spectrum of resistance to Phytophthora capsici conferred by a major effect quantitative trait locus (QTL) that has been detected in all of the resistant pepper accessions studied to date. After adding new markers derived from tomato sequences and those from pepper reported in the literature to three maps of pepper chromosome P5, we detected a QTL cluster involved in P. capsici resistance. By means of meta-analyses, we determined the occurrence of these QTLs in different genetic backgrounds and with different P.capsici isolates. Comparative mapping with tomato and potato highlighted a complex mosaic of Phytophthora resistance loci on colinear chromosome segments. We tested different lines with and without one of these QTLs, Pc5.1, with four isolates that we determined to be genetically distinct. Our data demonstrate that Pc5.1 is active against 12 isolates from different geographical origins and that it is conserved in all of the resistant accessions tested. We propose that this QTL is a key element responsible for the broad-spectrum resistance to P.capsici and, therefore, is a valuable locus for improving the effective resistance of pepper to P. capsici.

Development, Identification, and Genetic Analysis of a Quantitative Dwarfing Somatic Variation Line in Wheat

ABSTRACTDwarfing germplasms are crucial to the development of wheat (Triticum aestivum L.) varieties with ideal plant height and combinations of agronomic traits. A novel dwarfing wheat line, AS34, was developed in this study by somatic variation. This new wheat germplasm was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, two‐dimensional gel electrophoresis, genomic in situ hybridization, and genomic scanning with 44 simple sequence repeat (SSR) markers, and our analysis showed that AS34 was clearly derived from the somatic variation of Yumai66 (YM66), its tissue culture parent, but not from natural hybridization. Molecular tests using known primers specific to Rht8 and Rht‐B1b genes indicated that AS34 and its parent contained Rht8 but not Rht‐B1b in their genomes, which was not consistent with previous reports. Similar to YM66, AS34 was sensitive to gibberellic acid, and this characteristic might be induced only by Rht8 or by Rht8 and the new dwarfing genes simultaneously. Genetic analysis revealed that the new dwarfing trait in AS34 was controlled by multiple quantitative genes, and data from the F2 population yielded no key quantitative trait locus. According to the results of genomic scanning for different SSR markers, some of the new dwarfing genes in AS34 might be located on chromosome 4B. The new dwarfing material had positive effects on the agronomic traits related to grain yield in F2 populations, particularly the variation range in plant height. This dwarfing resource will be potentially used in wheat breeding for the development of new wheat varieties with available agronomic traits.

Identification of the quantitative trait loci (QTL) underlying water soluble protein content in soybean

Water soluble protein content (SPC) plays an important role in the functional efficacy of protein in food products. Therefore, for the identification of quantitative trait loci (QTL) associated with SPC, 212 F(2:9) lines of the recombinant inbred line (RIL) population derived from the cross of ZDD09454 × Yudou12 were grown along with the parents, in six different environments (location × year) to determine inheritance and map solubility-related genes. A linkage map comprising of 301 SSR markers covering 3,576.81 cM was constructed in the RIL population. Seed SPC was quantified with a macro-Kjeldahl procedure in samples collected over multiple years from three locations (Nantong in 2007 and 2008, Zhengzhou in 2007 and 2008, and Xinxiang in 2008 and 2009). SPC demonstrated transgressive segregation, indicating a complementary genetic structure between the parents. Eleven putative QTL were associated with SPC explaining 4.5-18.2 % of the observed phenotypic variation across the 6 year/location environments. Among these, two QTL (qsp8-4, qsp8-5) near GMENOD2B and Sat_215 showed an association with SPC in multiple environments, suggesting that they were key QTL related to protein solubility. The QTL × environment interaction demonstrated the complex genetic mechanism of SPC. These SPC-associated QTL and linked markers in soybean will provide important information that can be utilized by breeders to improve the functional quality of soybean varieties.

Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments

A large proportion of the worlds' wheat growing regions suffers water and/or heat stress at some stage during the crop growth cycle. With few exceptions, there has been no utilisation of managed environments to screen mapping populations under repeatable abiotic stress conditions, such as the facilities developed by the International Wheat and Maize Improvement Centre (CIMMYT). Through careful management of irrigation and sowing date over three consecutive seasons, repeatable heat, drought and high yield potential conditions were imposed on the RAC875/Kukri doubled haploid population to identify genetic loci for grain yield, yield components and key morpho-physiological traits under these conditions. Two of the detected quantitative trait loci (QTL) were located on chromosome 3B and had a large effect on canopy temperature and grain yield, accounting for up to 22 % of the variance for these traits. The locus on chromosome arm 3BL was detected under all three treatments but had its largest effect under the heat stress conditions, with the RAC875 allele increasing grain yield by 131 kg ha(-1) (or phenotypically, 7 % of treatment average). Only two of the eight yield QTL detected in the current study (including linkage groups 3A, 3D, 4D 5B and 7A) were previously detected in the RAC875/Kukri doubled haploid population; and there were also different yield components driving grain yield. A number of discussion points are raised to understand differences between the Mexican and southern Australian production environments and explain the lack of correlation between the datasets. The two key QTL detected on chromosome 3B in the present study are candidates for further genetic dissection and development of molecular markers.

Validation of DGAT1-2 polymorphisms associated with oil content and development of functional markers for molecular breeding of high-oil maize

The gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1-2) is a key quantitative trait locus that controls oil content and oleic acid composition in maize kernels. Here we re-sequenced the DGAT1-2 region responsible for oil variation in a maize landrace set and in 155 inbred lines (35 high-oil and 120 normal lines). The high-oil DGAT1-2 allele was present in most Northern Flint and Southern Dent populations but was absent in five of eight Corn Belt Dent open-pollinated populations and in most of the earlier inbred lines. Loss of the high-oil DGAT1-2 allele possibly resulted from genetic drift in the early twentieth century when a few Corn Belt Dent populations were selected for the development of high-grain-yield inbred lines. Association analysis detected significant effects of two PCR-based functional markers (HO06 and DGAT04; developed based on DGAT1-2 polymorphisms) on kernel oil content and oleic acid composition using the 155 inbred lines. Zheng58 and Chang7-2, the parent inbred lines of elite hybrid Zhengdan958, were used to transfer the favorable allele from the high-oil line By804 using marker-assisted backcrossing with the two functional markers. In BC5F2:3 populations, oil content of the three genotypes (−/−, +/−, and +/+) was, respectively, 3.37, 4.20, and 4.61% (Zheng58 recipient line) and 4.14, 4.67, and 5.25% (Chang7-2 recipient line). Oil content of homozygous kernels containing the high-oil DGAT1-2 allele increased by 27–37% compared with recurrent parents. Hence, these functional markers can be used to re-introduce the high-oil DGAT1-2 allele into modern inbred lines for increased oil content through marker-assisted backcrossing.

Ecological genetics and genomics of plant defences: evidence and approaches

Herbivores exert significant selection on plants, and plants have evolved a variety of constitutive and inducible defenses to resist and tolerate herbivory. Assessing the genetic mechanisms that influence defenses against herbivores will deepen our understanding of the evolution of essential phenotypic traits.Ecogenomics is a powerful interdisciplinary approach that can address fundamental questions about the ecology and evolutionary biology of species, such as: which evolutionary forces maintain variation within a population? and What is the genetic architecture of adaptation? This field seeks to identify gene regions that influence ecologically-important traits, assess the fitness consequences under natural conditions of alleles at key quantitative trait loci (QTLs), and test how the abiotic and biotic environment affects gene expression.Here, we review ecogenomics techniques and emphasize how this framework can address long-standing and emerging questions relating to anti-herbivore defenses in plants. For example, ecogenomics tools can be used to investigate: inducible vs. constitutive defenses; tradeoffs between resistance and tolerance; adaptation to the local herbivore community; selection on alleles that confer resistance and tolerance in natural populations; and whether different genes are activated in response to specialist vs. generalist herbivores and to different types of damage.Ecogenomic studies can be conducted with model species, such as Arabidopsis, or their relatives, in which case myriad molecular tools are already available. Burgeoning sequence data will also facilitate ecogenomic studies of non-model species. Throughout this paper, we highlight approaches that are particularly suitable for ecological studies of non-model organisms, discuss the benefits and disadvantages of specific techniques, and review bioinformatic tools for analyzing data.We focus on established and promising techniques, such as QTL mapping with pedigreed populations, genome wide association studies, transcription profiling strategies, population genomics, and transgenic methodologies. Many of these techniques are complementary and can be used jointly to investigate the genetic architecture of defense traits and selection on alleles in nature.

Characterization and precise mapping of a QTL increasing spike number with pleiotropic effects in wheat

Tiller number (TN) and spike number per plant (SN) are key components of grain yield and/or biomass in wheat. In this study, an introgression line 05210, developed by introgression of chromosomal segments from a synthetic exotic wheat Am3 into an elite cultivar Laizhou953, showed a significantly increased TN and SN, but shorter spike length (SL) and fewer grain number per spike (GNS) than Laizhou953. To investigate the quantitative trait locus (QTL) responsible for these variations, the introgressed segments in 05210 were screened by SSR markers and one follow-up segregation population was developed from the cross 05210/Laizhou953. The population showed 3:1 segregation ratios for SN, SL and GNS, indicating that QTLs for these traits have been dissected into single Mendelian factors. Bulked segregation analysis showed that the markers located on the 4B introgressed segment were polymorphic between the two bulks. Therefore, they were further analyzed in the F(2) population to construct a linkage map. Three new QTLs, QSn.sdau-4B, QSl.sdau-4B and QGns.sdau-4B, were detected for SN, SL and GNS, respectively, which explained a large portion of the phenotypic variation (30.1-67.6%) for these traits with overlapping peaks. Correlation analysis and multiple-trait, multiple-interval mapping (MMIM) suggested pleiotropic effects of the QTL on SN, SL and GNS. Therefore, the QTL was designated as QSn.sdau-4B. By a progeny test based on F(3) families using SN, the QTL was mapped as a Mendelian factor to the proximal region of 4BL. It is a key QTL responsible for variation in spike number and size, which had not been reported previously. Thus, it is an important QTL for wheat to achieve high and stable biomass and grain yield. Dissection and mapping of this QTL as a Mendelian factor laid a solid foundation for map-based cloning of grain yield-related QTLs in wheat.