水稻生物学产量及其构成性状的QTL定位

QTL的加性效应、加性×加性上位性效应及它们与环境的互作效应是数量性状的重要遗传分量.利用IR64/Azucena的125个DH品系为群体,分析了水稻生物学产量及其两个构成性状干草产量和谷粒产量的遗传组成.用基于混合模型的复合区间作图(MCIM)方法进行QTL定位.检测到12个位点有加性主效应,27个位点涉及双位点互作,18个位点存在环境互作.结果表明水稻生物学产量和它的两个构成性状普遍存在上位性效应和QE互作效应.此外,还探讨了性状间相关的遗传基础.发现4个QTLs和一对上位性QTLs可能与生物学产量与干草产量之间的正相关有关.3个QTL可能与干草产量与谷粒产量之间的负相关有关.这些结果可能部分地解释了这3个性状相关的遗传原因.通过对水稻生物学产量及其两个构成性状所定位QTL的分析,加深了对数量性状QTL的认识.首先,QTL的上位性效应和QE互作效应是普遍存在的;其次,QTL的多效性或紧密连锁可能是遗传相关的原因,当QTL对两个性状作用的方向相同时可导致正向遗传相关,反之则为负向遗传相关,当有些QTL表现为同向作用而另一些QTL表现为反向作用时,则可削弱性状间的遗传相关性;第三,复合性状的QTL效应可分解为其组成性状的QTL效应,如果QTL对各组成性状的效应方向相反而相互抵消,可使复合性状的QTL效应不易被检测;第四,加性效应的QTL常参预构成上位性效应,而具有上位性效应的QTL并非都有加性主效应,表明忽略上位性的QTL定位方法会降低检测QTL的功效;最后,鉴别不同类型的QTL效应有利于指导育种实践,选择主效QTL适用于多环境,QE互作QTL适用于特定环境,对上位性QTL应强调选择基因组合而并非单个基因.     

Mapping QTL for Biomass Yield and Its Components in Rice (Oryza sativa L.)

Addicive effects, additive by additive epistatic effects, and their environmental interactions of QTLs are important genetic components of quantitative traits. Genetic architecture underlying rice biomass yield and its two component traits (straw yield and grain yield) were analyzed for a population of 125 DH lines from an inter-subspecific cross of IR64/Azucena. The mixed-model based composite interval mapping approach (MCIM) was used to detect QTLs, There were 12 QTLs detected with additive main effects, 27 QTLs involved in digenic interaction with aa and/or aae effects, and 18 QTLs affected by environments with ae and/or aae effects. It was revealed that epistatic effects and QE interaction effects existed on biomass yield and its component traits in rice. In addition, the genetic basis of relationships among these traits were investigated. Four QTLs and one pair of epistatic QTLs were detected to be responsible for the positive correlation between biomass yield and straw yield. Three QTLs might be responsible for the negative correlation between straw yield and grain yield. This result could partially explain the genetic basis of correlation among the three traits, and provide useful information for genetic improvement of these traits by marker-assisted selection.     

Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe

Key message

Genome-wide association mapping as well as marker- and haplotype-based genome-wide selection unraveled a complex genetic architecture of grain yield with absence of large effect QTL and presence of local epistatic effects.

Abstract

The genetic architecture of grain yield determines to a large extent the optimum design of genomic-assisted wheat breeding programs. The main goal of our study was to examine the potential and limitations to dissect the genetic architecture of grain yield in wheat using a large experimental data set. Our study was based on phenotypic information and genomic data of 13,901 SNPs of a diverse set of 3816 elite wheat lines adapted to Central Europe. We applied genome-wide association mapping based on experimental and simulated data sets and performed marker- and haplotype-based genomic prediction. Computer simulations revealed for our mapping population a high power to detect QTL, even if they individually explained only 2.5% of the genetic variation. Despite this, we found no stable marker–trait associations when validating in independent subsets. A two-dimensional scan for marker–marker interactions indicated presence of local epistasis which was further supported by improved prediction abilities when shifting from marker- to haplotype-based genome-wide prediction approaches. We observed that marker effects estimated using genome-wide prediction approaches strongly varied across years albeit resulting in high prediction abilities. Thus, our results suggested that the prediction accuracy of genomic selection in wheat is mainly driven by relatedness rather than by exploiting knowledge of the genetic architecture.

     

Genetic dissection of developmental behavior of grain weight in wheat under diverse temperature and water regimes

As a quantitatively inherited trait related to high yield potential, grain weight (GW) development in wheat is constrained by abiotic stresses such as limited water supply and high temperature. Data from a doubled haploid population, derived from a cross of (Hanxuan 10?×?Lumai 14), grown in four environments were used to explore the genetic basis of GW developmental behavior in unconditional and conditional quantitative trait locus (QTL) analyses using a mixed linear model. Thirty additive QTLs and 41 pairs of epistatic QTLs were detected, and were more frequently observed on chromosomes 1B, 2A, 2D, 4A, 4B and 7B. No single QTL was continually active during all stages or periods of grain growth. The QTLs with additive effects (A-QTLs) expressed in the period S1|S0 (the period from the flowering to the seventh day after) formed a foundation for GW development. GW development at these stages can be used as an index for screening superior genotypes under diverse abiotic stresses in a wheat breeding program. One QTL, i.e. Qgw.cgb-6A.2, showed high adaptability for water-limited and heat-stress environments. Many A-QTLs interacted with more than one other QTL in the two genetic models, such as Qgw.cgb-4B.2 interacted with five QTLs, showing that the genetic architecture underlying GW development involves a collective expression of genes with additive and epistatic effects.     

大豆小区产量及其相关性状QTL间的上位性和环境互作效应

以晋豆23栽培大豆(Glycine max)为母本、灰布支黑豆(ZDD2315,半野生大豆)为父本衍生出447个RIL群体,通过构建SSR遗传图谱及利用混合线性模型分析方法,对2年大豆小区产量及主要植物学性状进行QTL定位,并作加性效应、加性×加性上位互作效应及环境互作效应分析。结果显示,共检测到12个与小区产量、单株粒重、单株茎重、单株粒茎比、有效分枝、主茎节数、株高和结荚高度相关的QTL,分别位于A1、A2、H_1、I、J_2和M连锁群上。其中小区产量、株高、单株粒重、有效分枝和主茎节数均表现为遗传正效应,即增加其性状的等位基因来源于母本晋豆23。同时,检测到11对影响小区产量、单株粒重、单株茎重、株高和结荚高度的加性×加性上位互作效应及环境互作效应的QTL,发现22个QTL与环境存在互作。实验结果表明,上位效应和QE互作效应对大豆小区产量及主要农艺性状的遗传影响很大。进行大豆分子标记辅助育种时,既要考虑效应起主要作用的QTL,又要注重上位性QTL,这样有利于性状的稳定表达和遗传。     

Epistatic interaction is an important genetic basis of grain yield and its components in maize

A population of 294 recombinant inbred lines (RIL) derived from Yuyu22, an elite maize hybrid extending broadly in China, has been constructed to investigate the genetic basis of grain yield, and associated yield components in maize. The main-effect quantitative trait loci (QTL), digenic epistatic interactions, and their interactions with the environment for grain yield and its three components were identified by using the mixed linear model approach. Thirty-two main-effect QTL and forty-four pairs of digenic epistatic interactions were detected for the four measured traits in four environments. Our results suggest that both additive effects and epistasis (additive × additive) effects are important genetic bases of grain yield and its components in the RIL population. Only 30.4% of main-effect QTL for ear length were involved in epistatic interactions. This implies that many loci in epistatic interactions may not have significant effects for traits alone but may affect trait expression by epistatic interaction with the other loci.     

Characterization of the main effects,epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice

Main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits. In this study, we analyzed the main effects, epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying four yield traits, using a population of 240 recombinant inbred lines from a cross between two rice varieties tested in replicated field trials. A genetic linkage map with 220 DNA marker loci was constructed. A mixed linear model approach was used to detect QTLs with main effects, QTLs involved in digenic interactions and QEs. In total, 29 QTLs of main effects, and 35 digenic interactions involving 58 loci were detected for the four traits. Thirteen QTLs with main effects showed QEs; no QE was detected for the QTLs involved in epistatic interactions. The amount of variations explained by the QTLs of main effect were larger than the QTLs involved in epistatic interactions, which in turn were larger than QEs for all four traits. This study illustrates the ability of the analysis to assess the genetic components underlying the quantitative traits, and demonstrates the relative importance of the various components as the genetic basis of yield traits in this population.     

Characterization of quantitative trait loci controlling genetic variation for preharvest sprouting in synthetic backcross-derived wheat lines

Aegilops tauschii, the wild relative of wheat, has stronger seed dormancy, a major component of preharvest sprouting resistance (PHSR), than bread wheat. A diploid Ae. tauschii accession (AUS18836) and a tetraploid (Triticum turgidum L. ssp. durum var. Altar84) wheat were used to construct a synthetic wheat (Syn37). The genetic architecture of PHS was investigated in 271 BC(1)F(7) synthetic backcross lines (SBLs) derived from Syn37/2*Janz (resistant/susceptible). The SBLs were evaluated in three environments over 2 years and PHS was assessed by way of three measures: the germination index (GI), which measures grain dormancy, the whole spike assay (SI), which takes into account all spike morphology, and counted visually sprouted seeds out of 200 (VI). Grain color was measured using both Chroma Meter- and NaOH-based approaches. QTL for PHSR and grain color were mapped and their additive and epistatic effects as well as their interactions with environment were estimated by a mixed linear-model approach. Single-locus analysis following composite interval mapping revealed four QTL for GI, two QTL for SI, and four QTL for VI on chromosomes 3DL and 4AL. The locus QPhs.dpiv-3D.1 on chromosome 3DL was tightly linked to the red grain color (RGC) at a distance of 5 cM. The other locus on chromosome 3D, "QPhs.dpiv-3D.2" was independent of RGC locus. Two-locus analysis detected nine QTL with main effects and 18 additive x additive interactions for GI, SI, and VI. Two of the nine main effects QTL and two epistatic QTL showed significant interactions with environments. Both additive and epistatic effects contributed to phenotypic variance in PHSR and the identified markers are potential candidates for marker-assisted selection of favorable alleles at multiple loci. SBLs derived from Ae. tauschii proved to be a promising tool to dissect, introgress, and pyramid different PHSR genes into adapted wheat genetic backgrounds. The enhanced expression of PHS resistance in SBLs enabled us to develop white PHS-resistant wheat germplasm from the red-grained Ae. tauschii accession.     

Post‐heading heat stress and yield impact in winter wheat of China

Wheat is sensitive to high temperatures, but the spatial and temporal variability of high temperature and its impact on yield are often not known. An analysis of historical climate and yield data was undertaken to characterize the spatial and temporal variability of heat stress between heading and maturity and its impact on wheat grain yield in China. Several heat stress indices were developed to quantify heat intensity, frequency, and duration between heading and maturity based on measured maximum temperature records of the last 50 years from 166 stations in the main wheat‐growing region of China. Surprisingly, heat stress between heading and maturity was more severe in the generally cooler northern wheat‐growing regions than the generally warmer southern regions of China, because of the delayed time of heading with low temperatures during the earlier growing season and the exposure of the post‐heading phase into the warmer part of the year. Heat stress between heading and maturity has increased in the last decades in most of the main winter wheat production areas of China, but the rate was higher in the south than in the north. The correlation between measured grain yields and post‐heading heat stress and average temperature were statistically significant in the entire wheat‐producing region, and explained about 29% of the observed spatial and temporal yield variability. A heat stress index considering the duration and intensity of heat between heading and maturity was required to describe the correlation of heat stress and yield variability. Because heat stress is a major cause of yield loss and the number of heat events is projected to increase in the future, quantifying the future impact of heat stress on wheat production and developing appropriate adaptation and mitigation strategies are critical for developing food security policies in China and elsewhere.     

Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

Key message

We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat.

Abstract

We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2–3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM^?2, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4–5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1–2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance.

     

Detection of epistatic interactions between exotic alleles introgressed from wild barley (H. vulgare ssp. spontaneum)

The expression of a quantitative phenotype can be controlled through genotype, environment and genotype by environment interaction effects. Further, genotype effects can be attributed to major genes, quantitative trait loci (QTL) and gene by gene interactions, which are also termed epistatic interactions. The present study demonstrates that two-way epistatic interactions can play an important role for the expression of domestication-related traits like heading date, plant height and yield. In the BC₂DH population S42, carrying wild barley introgressions in the genetic background of the spring barley cultivar Scarlett, 13, 8 and 12 marker by marker interaction effects could be detected for the traits heading date, plant height and yield, respectively. Significant allelic combinations at interacting loci coincided for heading date, plant height and yield suggesting the presence of pleiotropic effects rather than several linked QTL. The mode of epistasis observed was primarily characterised by either (1) compensatory effects, where allelic combinations from the same genotype buffered the phenotype, or (2) augmented effects, where only the combination of the exotic allele at both interacting loci caused an altered phenotype. The present study shows that estimates of main effects of QTL can be confounded by interactions with background loci, suggesting that the identification of epistatic effects is important for gene cloning and marker-assisted selection. Furthermore, interaction effects between loci and putative candidate genes detected in the present study reveal potential functional relationships, which can be used to further elucidate gene networks in barley.     

Detection of QTL for flowering time in multiple families of elite maize

Flowering time is a fundamental quantitative trait in maize that has played a key role in the postdomestication process and the adaptation to a wide range of climatic conditions. Flowering time has been intensively studied and recent QTL mapping results based on diverse founders suggest that the genetic architecture underlying this trait is mainly based on numerous small-effect QTL. Here, we used a population of 684 progenies from five connected families to investigate the genetic architecture of flowering time in elite maize. We used a joint analysis and identified nine main effect QTL explaining approximately 50?% of the genotypic variation of the trait. The QTL effects were small compared with the observed phenotypic variation and showed strong differences between families. We detected no epistasis with the genetic background but four digenic epistatic interactions in a full 2-dimensional genome scan. Our results suggest that flowering time in elite maize is mainly controlled by main effect QTL with rather small effects but that epistasis may also contribute to the genetic architecture of the trait.     

A three‐component system incorporating Ppd‐D1, copy number variation at Ppd‐B1, and numerous small‐effect quantitative trait loci facilitates adaptation of heading time in winter wheat cultivars of worldwide origin

The broad adaptability of heading time has contributed to the global success of wheat in a diverse array of climatic conditions. Here, we investigated the genetic architecture underlying heading time in a large panel of 1,110 winter wheat cultivars of worldwide origin. Genome‐wide association mapping, in combination with the analysis of major phenology loci, revealed a three‐component system that facilitates the adaptation of heading time in winter wheat. The photoperiod sensitivity locus Ppd‐D1 was found to account for almost half of the genotypic variance in this panel and can advance or delay heading by many days. In addition, copy number variation at Ppd‐B1 was the second most important source of variation in heading, explaining 8.3% of the genotypic variance. Results from association mapping and genomic prediction indicated that the remaining variation is attributed to numerous small‐effect quantitative trait loci that facilitate fine‐tuning of heading to the local climatic conditions. Collectively, our results underpin the importance of the two Ppd‐1 loci for the adaptation of heading time in winter wheat and illustrate how the three components have been exploited for wheat breeding globally.     

播种密度对秸秆覆盖旱地冬小麦产量和土壤水分的影响

为了解秸秆覆盖下作物群体对土壤水分和小麦产量的影响,于2012年6月至2013年6月在渭北旱塬研究秸秆覆盖与常规耕作模式下播种密度对土壤储水量、冬小麦群体动态变化、小麦产量及水分利用效率的影响。秸秆覆盖与常规耕作相比休闲期在0~3.6 m土层多蓄水105 mm,主要于小麦拔节后利用。不同播种密度主要影响小麦抽穗前的群体大小,抽穗后群体差异不显著。小麦籽粒产量为2 841~3 496 kg/hm, 不同密度水平或覆盖均没有显著影响小麦产量,但是高密度处理较中、低密度显著降低小麦收获指数。另外,秸秆覆盖小麦较常规增加20%耗水量,小麦水分利用效率降低11%。因此,在休闲期降雨丰富,生育期特旱的气候条件下播种密度对秸秆覆盖小麦产量没有影响,显著增加耗水量,降低水分利用效率。播种密度、秸秆覆盖及其交互效应还有待于在其他气候年型下进一步研究观测以便综合评价这些因素的影响效应,进而建立旱地小麦高产高效用水的管理措施。     

Gene action of canopy temperature in bread wheat under diverse environments

While canopy temperature (CT) shows a strong and reliable association with yield under drought and heat stress and is used in wheat breeding to select for yield, little is known of its genetic control. The objective of this study was to determine the gene action controlling CT in five wheat populations grown in diverse environments (heat, drought, and well-irrigated conditions). CT showed negative phenotypic correlations with grain yield under drought and well-irrigated environments. Additive × additive effects were most prevalent and significant for all crosses and environments. Dominance and dominance × dominance gene actions were also found, though the significance and direction was specific for each environment and genotypic cross. The use of CT as a selection criterion to improve tolerance to drought was supported by its significant association with grain yield and the genotype differences observed between cultivars. Our results indicated that genetic gains for CT in wheat could be achieved through conventional breeding. However, given some dominance and epistatic effects, it would be necessary to delay the selection process until the frequency of heterozygous loci within families is reduced.     

Simultaneous improvement of grain yield and protein content in durum wheat by different phenotypic indices and genomic selection

Key message

Simultaneous improvement of protein content and grain yield by index selection is possible but its efficiency largely depends on the weighting of the single traits. The genetic architecture of these indices is similar to that of the primary traits.

Abstract

Grain yield and protein content are of major importance in durum wheat breeding, but their negative correlation has hampered their simultaneous improvement. To account for this in wheat breeding, the grain protein deviation (GPD) and the protein yield were proposed as targets for selection. The aim of this work was to investigate the potential of different indices to simultaneously improve grain yield and protein content in durum wheat and to evaluate their genetic architecture towards genomics-assisted breeding. To this end, we investigated two different durum wheat panels comprising 159 and 189 genotypes, which were tested in multiple field locations across Europe and genotyped by a genotyping-by-sequencing approach. The phenotypic analyses revealed significant genetic variances for all traits and heritabilities of the phenotypic indices that were in a similar range as those of grain yield and protein content. The GPD showed a high and positive correlation with protein content, whereas protein yield was highly and positively correlated with grain yield. Thus, selecting for a high GPD would mainly increase the protein content whereas a selection based on protein yield would mainly improve grain yield, but a combination of both indices allows to balance this selection. The genome-wide association mapping revealed a complex genetic architecture for all traits with most QTL having small effects and being detected only in one germplasm set, thus limiting the potential of marker-assisted selection for trait improvement. By contrast, genome-wide prediction appeared promising but its performance strongly depends on the relatedness between training and prediction sets.

     

Characterization of a Putative New Semi-Dominant Reduced Height Gene,Rht_NM9, in Wheat(Triticum aestivum L.)

Plant height is an important agronomic trait in cereal crops, and can affect both plant architecture and grain yield. New dwarfing genes are required for improving the genetic diversity of wheat. In this study, a novel dwarf mutant, NM9, was created by treating seeds of the wheat variety NAU9918 with ethyl methanesulfonate(EMS). NM9 showed obvious phenotypic changes, which were distinct from those caused by other dwarfing genes, especially the reduced plant height, increased effective tiller number, and elongated spike and grain length. The reduced plant height in NM9 was attributable to a semi-dominant dwarfing gene Rht_NM9, which was flanked by two closely linked SNP markers, SNP34 and SNP41, covering an 8.86-Mb region on the chromosome arm 2AS. The results of gibberellic acid(GA) sensitivity evaluation, comparative genomics analysis and allelism test indicated that Rht_NM9 was neither allelic to Rht7 and Rht21 nor homoeoallelic to Rht8, so Rht_NM9 was proposed to be a new dwarfing locus on the homoeologous group 2 chromosomes of wheat. Rht_NM9has a negative effect on plant height and positive effects on effective tiller number and grain size, thus, Rht_NM9 could be used for elucidating the mechanisms underlying plant architecture and grain development.     

Replication and explorations of high-order epistasis using a large advanced intercross line pedigree

Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts, much remains unclear including the role and importance of genetic interactions. This study provides empirical evidence for a strong and persistent contribution of both second- and third-order epistatic interactions to long-term selection response for body weight in two divergently selected chicken lines. We earlier reported a network of interacting loci with large effects on body weight in an F(2) intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL). The original report showed an important contribution of capacitating epistasis to growth, meaning that the genotype at a hub in the network releases the effects of one or several peripheral loci. After fine-mapping of the loci in the AIL, we show that these interactions were persistent over time. The replication of five of six originally reported epistatic loci, as well as the capacitating epistasis, provides strong empirical evidence that the originally observed epistasis is of biological importance and is a contributor in the genetic architecture of this population. The stability of genetic interaction mechanisms over time indicates a non-transient role of epistasis on phenotypic change. Third-order epistasis was for the first time examined in this study and was shown to make an important contribution to growth, which suggests that the genetic architecture of growth is more complex than can be explained by two-locus interactions only. Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait.     

二棱大麦熟期性状的遗传研究

以甘木二条等7个二棱大麦品种进行不完全双列杂交,对其亲本、F1和F2的抽穗期,灌浆期和成熟期三个性状以1992和1995年（播种年份）的两年资料,采用加性-显性-上位性（ADAA）模型进行遗传分析．遗传方差分量的比率估算表明,三个性状都存在上位性作用．除灌浆期外,其余二性状还受显性和加性效应的作用,并以加性为主．显性效应和加性效应与环境的互作均达显著水平,基因效应的预测值表明采用P3（黔浙1号）和P4（浙农大3号）较易获得早熟后代．