Genetic control systems of stem branching and plant height in linseed

A diallel analysis of the traits “plant height”, “number of lateral stems”, and “number of lateral shoots” was carried out using Hayman’s method in three self-pollinated lines and one linear cultivar of linseed. A similarity was demonstrated between the inheritance of the studied traits and the additive-dominant model without any nonallelic interactions. The recessive nature of inheritance of increased plant height and high numbers of shoots together with dominant inheritance of increased numbers of lateral stems was revealed. The number of blocks of polymeric genes responsible for the variability in the studied traits was also estimated. The lines of linseed were ranged according to their contents of dominant alleles.     

Combining ability for the traits of stem branching and plant height in linseed lines

Combining ability for the traits of stem branching and plant height has been studied in ten pure lines of flax under complete and incomplete diallel crosses. High heritability of the traits "plant height", "the number of lateral stems" and "the number of lateral shoots" and essential role of genes with dominant effects of interaction in genetic control of the traits of stem branching and plant height have been shown. On the basis of combining ability indexes the ways for usage of certain genotypes and crossing combinations in flax breeding were defined. As a result of individual selection from hybrid combinations some new complexes of habit traits and agriculturally valuable plant characteristics were obtained.     

Combining ability according to the traits of stem branching and plant height in linseed lines

The combining ability according to the traits of stem branching and plant height has been studied for ten pure lines of oil flax under the conditions of complete and incomplete diallel crosses. The high heritability of traits, such as plant height, the number of lateral stems and shoots, and the essential role of genes with dominant effects of interaction in genetic control of the traits of stem branching and plant height have been shown. The methods of application of certain genotypes and crossed combinations in flax breeding based on combining-ability indexes were identified. Some new complexes of habitus traits and agriculturally valuable plant characteristics were obtained as a result of individual selection from hybrid combinations.     

标准切花菊杂交F1代群体侧枝侧蕾性状的杂种优势和遗传分析

以标准切花菊〔Dendranthema morifolium(Ramat.)Tzvel.〕品种'优香'('Yuuka')为母本、品种'神马'('Jinba')为父本进行杂交,对杂交F1代群体的单株侧枝平均长度、单株侧枝数、单株侧枝数与单株叶节数的比值(R1)、主蕾直径与侧蕾直径的比值(R2)、单株侧蕾数以及主蕾与侧蕾间距离6个性状进行杂种优势和相关性分析,并利用主基因+多基因混合遗传模型检测这些性状的主基因效应.结果显示:杂交F1代群体6个侧枝侧蕾性状的变异系数为2378%~5065%,且侧枝性状的变异系数总体上高于侧蕾性状;各性状的频次均呈现连续性的正态分布趋势,说明这些性状可能属于多基因控制的数量性状.杂交F1代群体的6个侧枝侧蕾性状均在001水平上表现出显著的中亲优势,表明各性状均存在显著的杂种优势.6个性状中,单株侧枝平均长度的中亲值最大(6230 mm),R1的中亲值最小(026);单株侧枝平均长度、R2和主蕾与侧蕾间距离的中亲优势均为正值,单株侧枝数、单株侧蕾数和R1的中亲优势均为负值.6个性状的中亲优势率为-5374%~3128%,其中,单株侧枝数的中亲优势率最小,而主蕾与侧蕾间距离的中亲优势率最大.相关性分析结果显示:单株侧枝平均长度和单株侧枝数均与R1呈极显著正相关,并与R2和单株侧蕾数呈极显著负相关;R2与侧蕾数也呈极显著正相关,且二者均与主蕾与侧蕾间距离呈极显著正相关.混合遗传分析结果显示:单株侧枝平均长度、R1、R2和单株侧蕾数均受2对主基因控制,符合B-1模型,主基因表现为"加性-显性-上位性",这4个性状的遗传率分别为7707%、9672%、6438%和5307%;单株侧枝数也受2对主基因控制,符合B-2模型,主基因表现为"加性-显性",该性状的遗传率为7438%,表明这5个性状的遗传存在主基因控制效应.而主蕾与侧蕾间距离符合A-0遗传模型,说明该性状无主基因控制,易受环境影响.     

Effects of intervarietal genetic heterogeneity in oats by results of F1 diallele analysis

Genetic analysis of seven oat varieties for eight traits which are the yield components was performed when studying the varieties and the F1 hybrids from their diallel crosses. Involvement of epistatic genes in genetic control of all the traits excluding the panicle density was established. By analysing the diallel tables with excluded data from the varieties with epistatic genes, it was revealed that hyperdominance is inherent to genetic control of the majority of traits studied. The dominant gene action exceeds the additive gene action. The genes "u" increasing the phenotypic displaying of the trait are always dominant and their frequency in the variety set under consideration is higher than the frequency of the genes "v" for all traits studied.     

Analysis of an introgressed Nicotiana tomentosa genomic region affecting leaf number and correlated traits in Nicotiana tabacum

Germplasm from closely related diploid relatives of tobacco (Nicotiana tabacum L.) could be of value for continued genetic modification of this species and for mapping quantitative trait loci (QTLs). We examined near isogenic tobacco lines and hybrids differing for an introgressed genomic region from N. tomentosa Ruiz and Pavon designated as Many Leaves that exhibits a large influence on leaf number and correlated traits. Within a ‘Red Russian’ genetic background, the region acted in an additive to partially dominant fashion to delay flowering time, and increase leaf number, plant height, and green leaf yield. Evidence of epistasis was observed as the region affected these traits to varying degrees in diverse near isogenic hybrids. Fifteen amplified fragment length polymorphism (AFLP) markers of N. tomentosa origin were mapped within a single linkage group of 34.5 cM using a population of 207 BC₁F₁ individuals segregating for Many Leaves. Composite interval mapping produced 2–LOD confidence intervals for likely QTL positions influencing leaf number (3.1 cM region), plant height (2.9 cM region), and days to flowering (3.3 cM region). These intervals were overlapping. Results demonstrate that genomic regions with large genetic effects can be transferred to tobacco from closely related diploid relatives, and that sufficient recombination within these regions may permit mapping of genes controlling quantitative traits. Materials and results described here may be useful in future research to gain insight on the genetic control of the transition from vegetative to reproductive development in Nicotiana.     

Genetic control system of the differences in duration of vernalization in winter common wheat

Hypotheses of differences in genetic control on duration of vernalization for winter wheat have been considered. It has been shown that differences in this character are controlled by independent Vrd gene system. Monogenic dominant near-isogenic lines have been created. They differ in two non-allelic Vrd1 and Vrd2 genes with unequal expression. The response of created lines to photoperiodic changes and Vrd genes effects on various agronomic traits have been characterized. Vrd genotypes have been identified in a number of winter common wheat cultivars.     

Mass spectrometry analysis of the variants of histone H3 and H4 of soybean and their post-translational modifications

Background

Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes. Mutagenised plant populations are one such resource that facilitate gene characterisation. They allow complex physiological responses to be correlated with the expression of single genes in planta, through either reverse genetics where target genes are mutagenised to assay the affect, or through forward genetics where populations of mutant lines are screened to identify those whose phenotype diverges from wild type for a particular trait. One limitation of these types of populations is the prevalence of gene redundancy within plant genomes, which can mask the affect of individual genes. Activation or enhancer populations, which not only provide knock-out but also dominant activation mutations, can facilitate the study of such genes.

Results

We have developed a population of almost 50,000 activation tagged A. thaliana lines that have been archived as individual lines to the T₃ generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Insertion site sequences have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes, provisional data identifying novel alleles and genes controlling steps in proanthocyanidin biosynthesis and trichome development is presented.

Conclusion

This publicly available population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterised genes annotated within the Arabidopsis genome sequence http://aafc-aac.usask.ca/FST. The presence of enhancer elements on the inserted T-DNA molecule allows both knock-out and dominant activation phenotypes to be identified for traits of interest.     

Analysis of the effects of parental genotypes of rye lines on the development of quantitative traits in primary octaploid triticale. Plant height

When breeding the primary spring octoploid triticale derived from crosses of various inbred rye lines to wheat Chinese Spring, the effects of the rye genotype and growth conditions on the plant height and proportion of the first, second, and final (pedicle) internodes to the entire stem length were studied. Two triticale groups were examined: homozygotes for the dominant (Ddw1) and recessive (ddw1) alleles of the gene responsible for short stem in rye. In the short stem triticale lines carrying the Ddw1 alleles, the plants were 20 cm shorter on average than those in the ddw1-carrying lines, and the distribution of the two triticale groups overlapped significantly. In both groups, the lines significantly differing in plant height could be differentiated, because of allelic diversity of the additional genes controlling this trait along with the Ddw gene. In most triticale lines, especially in the Ddw1-carrying ones, the plant height was much reduced under unfavorable growth conditions. At the same time, a short-stem line was isolated, which is characterized by ecological plasticity, like the maternal wheat cultivar. In the triticale studied, the stem structure depended on the short-stem rye genotype. The two-year study showed that in the triticale carrying the dominant allele of this gene, the first internode is significantly extended, whereas the upper (pedicle) internode is reduced, which increases plant lodging resistance. The differences revealed between the rye lines as well as their effect on the quantitative triticale traits are discussed in view of a variant of the hybridological analysis, which had been previously proposed for identification and mapping of the correspondent rye genes.     

Identification and utilization of genetic determinants of trait measurement errors in image-based,high-throughput phenotyping

The accuracy of trait measurements greatly affects the quality of genetic analyses. During automated phenotyping, trait measurement errors, i.e. differences between automatically extracted trait values and ground truth, are often treated as random effects that can be controlled by increasing population sizes and/or replication number. In contrast, there is some evidence that trait measurement errors may be partially under genetic control. Consistent with this hypothesis, we observed substantial nonrandom, genetic contributions to trait measurement errors for five maize (Zea mays) tassel traits collected using an image-based phenotyping platform. The phenotyping accuracy varied according to whether a tassel exhibited “open” versus. “closed” branching architecture, which is itself under genetic control. Trait-associated SNPs (TASs) identified via genome-wide association studies (GWASs) conducted on five tassel traits that had been phenotyped both manually (i.e. ground truth) and via feature extraction from images exhibit little overlap. Furthermore, identification of TASs from GWASs conducted on the differences between the two values indicated that a fraction of measurement error is under genetic control. Similar results were obtained in a sorghum (Sorghum bicolor) plant height dataset, demonstrating that trait measurement error is genetically determined in multiple species and traits. Trait measurement bias cannot be controlled by increasing population size and/or replication number.

The accuracy of high-throughput phenotyping can be affected by genetically determined measurement biases, which can alter the results of genetic analyses.     

Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations

To understand the types of gene action controlling seven quantitative traits in rice, QTL mapping was performed to dissect the main effect (M-QTLs) and digenic epistatic (E-QTLs) QTLs responsible for the trait performance of 254 recombinant inbred lines (RILs) of "Lemont/Teqing", and two testcross (TC) F(1) populations derived from these RILs. The correlation analyses reveal a general pattern, i.e. trait heritability in the RILs was negatively correlated to trait heterosis in the TC hybrids. A large number of M-QTLs and E-QTLs affecting seven traits, including heading date (HD), plant height (PH), flag leaf length (FLL), flag leaf width (FLW), panicle length (PL), spikelet number per panicle (SN) and spikelet fertility (SF), were identified and could be classified into two predominant groups, additive QTLs detected primarily in the RILs, and overdominant QTLs identified exclusively in the TC populations. There is little overlap between QTLs identified in the RILs and in the TC populations. This result implied that additive gene action is largely independent from non-additive gene action in the genetic control of quantitative traits of rice. The detected E-QTLs collectively explained a much greater portion of the total phenotypic variation than the M-QTLs, supporting prior findings that epistasis has played an important role in the genetic control of quantitative traits in rice. The implications of these results to the development of inbred and hybrid cultivars were discussed.     

Molecular marker-facilitated studies in an elite maize population: I. Linkage analysis and determination of QTL for morphological traits

Restriction fragment length polymorphisms (RFLPs) and one morphological marker were used to investigate quantitative trait loci (QTL) for morphological and physiological traits evaluated on 150 F₂₃ maize (Zea mays L.) lines derived from the cross of elite U.S. Corn Belt inbreds Mo17 and H99. F₂₃ lines were grown in a replicated experiment and evaluated for plant and ear heights and flowering traits. QTL were identified for each trait, and genetic effects were determined. Estimated gene action for the flowering traits was predominantly overdominance. Both parents contributed toward increased values for anthesis and silk emergence. QTL for increased plant and ear heights were usually contributed by the taller parent, Mo17. Estimated gene action for these traits was mainly partial to overdominance. QTL for plant height were located in the vicinity of loci defined by alleles with qualitative effects on plant height.     

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Background

Sorghum is a tropical C₄ cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation.

Results

We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time.

Conclusions

Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.     

Multiple-line cross QTL mapping for biomass yield and plant height in triticale (× Triticosecale Wittmack)

Key message

QTL mapping in multiple families identifies trait-specific and pleiotropic QTL for biomass yield and plant height in triticale.

Abstract

Triticale shows a broad genetic variation for biomass yield which is of interest for a range of purposes, including bioenergy. Plant height is a major contributor to biomass yield and in this study, we investigated the genetic architecture underlying biomass yield and plant height by multiple-line cross QTL mapping. We employed 647 doubled haploid lines from four mapping populations that have been evaluated in four environments and genotyped with 1710 DArT markers. Twelve QTL were identified for plant height and nine for biomass yield which cross-validated explained 59.6 and 38.2 % of the genotypic variance, respectively. A major QTL for both traits was identified on chromosome 5R which likely corresponds to the dominant dwarfing gene Ddw1. In addition, we detected epistatic QTL for plant height and biomass yield which, however, contributed only little to the genetic architecture of the traits. In conclusion, our results demonstrate the potential of genomic approaches for a knowledge-based improvement of biomass yield in triticale.     

Influence of rol genes in floriculture

Traditionally, new traits have been introduced into ornamental plants through classical breeding. However, genetic engineering now enables specific alterations of single traits in already successful varieties. New or improved varieties of floricultural crops can be obtained by acting on floral traits, such as color, shape or fragrance, on vase life in cut-flower species, and on rooting potential or overall plant morphology. Overexpression of the rol genes of the Ri plasmid of Agrobacterium rhizogenes in plants alters several of the plant's developmental processes and affects their architecture. Both A. rhizogenes- and rol-transgenic plants display the "hairy-root phenotype", although specific differences are found between species and between transgenic lines. In general, these plants show a dwarfed phenotype, reduced apical dominance, smaller, wrinkled leaves, increased rooting, altered flowering and reduced fertility. Among the rol genes, termed rolA, B, C and D, rolC has been the most widely studied because its effects are the most advantageous in terms of improving ornamental and horticultural traits. In addition to the dwarfness and the increase in lateral shoots that lead to a bushy phenotype, rolC-plants display more, smaller flowers, and advanced flowering; surprisingly, these plants may have better rooting capacity and they show almost no undesirable traits. rolD, the least studied among the rol genes, offers promising applications due to its promotion of flowering. Although the biochemical functions of rol genes remain poorly understood, they are useful tools for improving ornamental flowers, as their expression in transgenic plants yields many beneficial traits.     

Metabolomics analysis and metabolite‐agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines

Plants produce numerous metabolites that are important for their development and growth. However, the genetic architecture of the wheat metabolome has not been well studied. Here, utilizing a high‐density genetic map, we conducted a comprehensive metabolome study via widely targeted LC‐MS/MS to analyze the wheat kernel metabolism. We further combined agronomic traits and dissected the genetic relationship between metabolites and agronomic traits. In total, 1260 metabolic features were detected. Using linkage analysis, 1005 metabolic quantitative trait loci (mQTLs) were found distributed unevenly across the genome. Twenty‐four candidate genes were found to modulate the levels of different metabolites, of which two were functionally annotated by in vitro analysis to be involved in the synthesis and modification of flavonoids. Combining the correlation analysis of metabolite‐agronomic traits with the co‐localization of methylation quantitative trait locus (mQTL) and phenotypic QTL (pQTL), genetic relationships between the metabolites and agronomic traits were uncovered. For example, a candidate was identified using correlation and co‐localization analysis that may manage auxin accumulation, thereby affecting number of grains per spike (NGPS). Furthermore, metabolomics data were used to predict the performance of wheat agronomic traits, with metabolites being found that provide strong predictive power for NGPS and plant height. This study used metabolomics and association analysis to better understand the genetic basis of the wheat metabolism which will ultimately assist in wheat breeding.     

玉米株高和穗位高的遗传基础与分子机制*

株高和穗位高是玉米重要育种性状,直接影响植株的养分利用效率及抗倒伏性,进而影响玉米产量。玉米株高和穗位高属于典型数量性状,目前通过数量性状位点(quantitative trait loci mapping,QTL)定位和全基因组关联分析(genome-wide association study, GWAS)等方法已挖掘到较多相关遗传位点,通过QTL精细定位及利用突变体克隆了一些调控株高和穗位高关键基因。但是由于各研究组所利用的群体类型和大小、标记类型和密度以及统计方法不同,所鉴定QTL差异较大,单个研究难以揭示玉米株高和穗位高遗传结构。早期QTL定位的结果多以遗传距离来展示,不同时期GWAS研究所使用参考基因组版本不同,这进一步增加了借鉴和利用前人研究结果的难度。首次将目前已鉴定株高和穗位高遗传定位信息统一锚定至玉米自交系B73参考基因组V4版本,构建了株高和穗位高性状定位的一致性图谱,并鉴定出可被多个独立研究定位的热点区间。进一步对已克隆玉米株高和穗位高调控基因进行总结与分类,揭示株高和穗位高性状调控机制,对深度解析株高和穗位高遗传结构、指导基因克隆和利用分子标记辅助选择优化玉米株高和穗位高性状均具有重要意义。     

Genetic-statistical characterization of the novel different-height donors of the stem shortness in winter rye

Three donors for the dominant stem shortness in winter rye were developed. The genetic determination of the difference in a plant height for each donor was revealed. There were additive genes for the stem shortness in the donors Gnom 1 and Gnom 2 and dominant-epistatic ones in the donor Gnom 3. The investigation of genetic correlation between the number of quantitative traits and the plant height was carried out. On the basis of the data obtained, the strategy of using each donor for stem shortness in rye breeding was determined.     

Estimates of broad-sense heritability for seed yield and yield criteria in faba bean (Vicia faba L.)

Eight faba bean (Vicia faba L.) genotypes were grown at lowlands of the west-Mediterranean region of Turkey in order to estimate the broad-sense heritability for plant height, number of stems and pods per plant, seed yield, biological yield, 100-seed weight, days to flowering and maturity. The heritability for plant height, number of stems and pods per plant, seed yield, biological yield, 100-seed weight, days to flowering and maturity were estimated as 83%, 63%, 43%, 62%, 52%, 99%, 97% and 97%, respectively. It was found that seed weight was the least affected trait across changing environmental conditions and followed by days to flowering and maturity. On the other hand, number of pods per plant, biological and seed yields and number of stems per plant were the most affected traits versus environmental conditions.     

水稻幼苗活力性状的低温反应数量性状基因座检测

以籼粳交“密阳23/吉冷1号”的F2：3代200个家系作为作图群体,在12℃冷水胁迫下,进行苗高、苗鲜重和苗干重等水稻幼苗活力性状的低温反应鉴定,并利用由SSR标记构建的分子连锁图谱为基础,对冷水胁迫下苗高、苗鲜重和苗干重以及它们的低温反应指数进行了数量性状基因座（QTLs）检测。研究结果表明,低温胁迫下上述幼苗活力性状在F3家系群中均表现为接近正态的连续分布,表现为由多基因控制的数量性状;在第1、2、7、8和12染色体上,检测到与幼苗活力性状的低温反应相关的QTL共12个,对表型变异的贡献率范围为5．2％-17．9％,其中位于第2染色体RM262-RM263区间和第12染色体RM270-RM17区间的与低温下苗高相关的qCSH2和qCSH12,以及位于第12染色体RM19-RM270区间和第1染色体RM129-RM9区间的分别控制低温下苗干重及其低温反应指数的qSDW12和qCSDW1对表型变异的贡献率较大,分别为16．6％、17．9％、15．9％和16．2％。其增效等位基因均来自吉冷1号,前两者均表现为加性效应,后两者分别表现为显性和超显性。