利用WGCNA鉴定玉米株高和穗位高基因共表达模块

株高和穗位高是玉米株型的重要影响因子,与产量性状紧密相关。加权基因共表达网络分析(weightedgene co-expression network analysis, WGCNA)是探索基因网络与特定性状间关联关系的重要方法,为株高和穗位高相关基因的挖掘提供新途径。本研究利用郑58、掖478、昌7-2和黄早四及其组配的杂交种郑单958、安玉5号、郑58/黄早四和掖478/黄早四,结合其在45,000株hm~(–2)和67,500株hm~(–2)条件下的转录组数据,采用WGCNA构建了2种密度条件下的共表达网络,分别得到24个和21个共表达模块,并鉴定到与株高和穗位高显著且高度相关(相关系数的绝对值0.50)的共表达模块15个,其中两性状相同的模块共6个。基因功能富集分析结果表明,株高和穗位高共表达模块主要参与生长发育、光合作用、响应光刺激、植物激素、碳水化合物合成/代谢等重要活动。根据模块内基因的连接度,发现乙烯响应因子EREB14、硫胺素酶TENA2、磷酸甘油酸激酶PGK、谷胱甘肽转移酶GST2和琥珀酸脱氢酶SUDH7等是模块内的核心基因。通过构建其局部网络,发现EREB14与已报道株高基因D8、DWF1和ZmGRF10以及C3H转录因子C3H35、C2C2-GATA转录因子GATA4和乙烯受体同源子ETR40等存在关联关系。此外,已报道株高基因An1和GA20ox3也存在于共表达模块中。以这5个已报道株高基因为核心,构建其基因网路,发现生长素转录因子ARFTF7、ARFTF26、GST39、光合系统II氧进化多肽PspB2和光合系统IN亚基PasN1等与其存在关联。15个共表达模块和核心基因的挖掘以及基因生物学功能和互作网络的解析有助于揭示玉米株高和穗位高的遗传基础。     

基于QTL定位和全基因组关联分析筛选甘蓝型油菜株高和一次有效分枝高度的候选基因

株高和一次有效分枝高度是与甘蓝型油菜结荚层厚度、收获指数紧密关联的重要农艺性状,有关株高的数量性状位点(quantitative trait locus,QTL)和全基因组关联分析(genome-wide association study,GWAS)已有很多报道,但对一次有效分枝高度的QTL和GWAS定位以及候选基因筛选的研究报道较少。本研究利用已构建的高密度遗传连锁图对2016和2017年2个环境的186个株系组成的重组自交系群体株高和一次有效分枝高度及其最佳线性无偏预测(best linear unbiased prediction,BLUP)值进行QTL定位共检测到8个株高的QTL,分别位于A03、A04和A09染色体,单个QTL解释4.60%~13.29%的表型变异,其中位于A04染色体上的QTL(q-2017PH-A04-2和q-BLUP-PH-A04-2)在2017年和BLUP中均被检测到;检测到9个一次有效分枝高度QTL,分别位于A01、A02、A05、A09、C01和C05染色体上,单个QTL解释5.12%~19.10%的表型变异,其中q-2017BH-A09-1、q-BLUP-BH-A09-2和q-BLUP-BH-A09-3有重叠区段。同时,利用课题组前期完成的588份重测序自然群体进行全基因组关联分析,2年共检测到与株高显著关联的50个SNP位点和与一次有效分枝高度显著关联的12个SNP位点;根据SNP的物理位置,筛选出参与细胞增殖、细胞扩增、细胞周期和细胞壁活动的13个株高候选基因,以及参与赤霉素、亚精胺等合成代谢途径、核糖体组成和在光合、萌发等过程中有一定作用的一次分枝高度的11个候选基因,并利用荧光定量PCR技术验证候选基因在极端材料中的表达情况。本研究结果将为油菜株型改良及后续基因的功能研究提供理论依据。     

Inheritance of reduced plant height in the sunflower line Dw 89

The objective of the present research was to study the inheritance of reduced plant height in the sunflower line Dw 89. Plants of the cytoplasmic male sterile version of this line, cmsDw 89 (mean plant height of 47.4 cm) were crossed with plants of the restorer line RHA 271 (mean of 120.9 cm). F₁ plants averaged 120.4 cm, which indicated dominance of standard over reduced plant height. F₂ plants followed a segregation pattern of 1 : 15 (reduced : normal height), suggesting that reduced plant height in Dw 89 is controlled by alleles at two loci, designated Dw1 and Dw2. Class assignment in the F₂ was confirmed through the evaluation of the F₃ generation. Backcrosses to Dw 89 segregated with 1 : 3 (reduced : normal height) ratios, which confirmed the digenic inheritance of the trait. The evaluation of plant height distributions in F₃ families suggested possible genetic interaction between the Dw1 and Dw2 loci.     

Breeding long coleoptile, reduced height wheats

Semidwarf wheats have the potential to produce high yields when sown and managed under optimal conditions. However, farm yields often fall below this potential because of poor seedling establishment and low early vigour associated with gibberellic acid (GA)-insensitive reducing-height ( Rht) genes contained in these wheats. Australian and overseas wheats containing major and minor Rht genes sensitive to GA were intercrossed to develop three populations. Seedlings sensitive to GA and therefore lacking Rht-B1b ( Rht1) and Rht-D1b ( Rht2) plant height genes were selected for further study. GA- sensitive F4-derived lines were sown in field and glasshouse environments to determine plant height, and then sown at four temperatures to determine coleoptile length. Genetic variation in plant height and coleoptile length was large and significant ( P<0.01) among lines within each population with a number of lines identified as producing plant heights as short as current semidwarf varieties. Transgressive segregation for coleoptile length produced progenies with coleoptiles significantly ( P < 0.05) longer than the longest coleoptile parent in each population. Genotype × temperature interactions for coleoptile length were small thereby resulting in high line-mean heritabilities (h2 = 85–89) for this character. Larger plant-to-plant variation reduced single-plant estimates of heritability for plant height (h2 = 29–31) but heritability was increased (h2 = 68–78) with replication within and over environments. High narrow-sense heritabilities indicate that phenotypic selection should produce modest genetic gain for both characters. Variation in coleoptile length was poorly related to differences in plant height (r2 = 0.00 to 0.04 ns) while selection differentials for plant height were not associated with any change in coleoptile length of the selected groups. When considered together, height and coleoptile length appeared to be largely under independent genetic control among GA-sensitive wheats. These results suggest that GA-sensitive Rht genes could be used to select shorter height, longer-coleoptile wheats with improved establishment and seedling vigour. This revised version was published online in July 2006 with corrections to the Cover Date.     

控制高粱分蘖与主茎株高一致性的基因定位

用分蘖与主茎株高一致的高粱品系K35-Y5与分蘖明显高于主茎的高粱恢复系1383杂交, F1自交获得F2分离群体,构建两混池,采用BSA (bulked segregation analysis)和SLAF (specific length amplified fragment sequencing)技术将高粱分蘖与主茎株高一致基因定位。遗传分析表明,分蘖与主茎株高一致性状由1对隐性核基因控制。参考已公布高粱基因组设计酶切方案,构建SLAF文库并测序。对高粱参考基因组序列进行电子酶切预测,确定限制性内切酶为Rsa I+Hae III,酶切片段长度为364～414 bp;测序Q30为91.70%, GC含量为45.79%,达到测序要求;与水稻的测序数据相比,高粱的双端比对效率为93.35%,酶切效率为90.60%, SLAF建库正常。共获得30.80 M reads,开发出133,246个SLAF标签,再通过分析SLAF标签的多态性,检测到319,428个SNP位点。利用SNP-index法和Euclideandistance法及取两者交集进行关联分析,最后得到一个关联区域,位于第9染色体上的54,788,026～56,740,873区间内,关联区域长度1.95 Mb。分析关联区域内的基因在2个亲本之间SNP,对这些SNP进行变异的注释,发现4个非同义突变的SNP。经验证,这4个SNP位点和分蘖与主茎株高一致性状相关。对应到Sobic.009G197901.1、Sobic.009G213300.1和Sobic.009G221200.1三个基因上,这些基因可能是与性状直接相关的功能基因。     

Interrelationships among height,lodging and yield in determinate and indeterminate soybeans

Summary Seventy-three determinate and 93 indeterminate random F₉ lines from a cross between determinate and indeterminate soybean [Glycine max (L.) Merr.] parents were evaluated for seed yield, mature plant height, and lodging. Regression analyses indicated that among the determinate lines, seed yield increased by 350 kg/ha and lodging score increased by 0.008 for every 10 cm increase in plant height. Among indeterminate lines seed yield increased by 112 kg/ha and lodging score by 0.3 for every 10 cm increase in plant height. The highest yielding indeterminate lines were tall and very susceptible to lodging. The tall determinate lines had the best combination of high seed yield and excellent lodging resistance.Cooperative Investigations of the Science and Education Administration, U.S. Department of Agriculture and the Purdue University Agricultural Experiment Station.     

Dynamic QTL mapping for plant height in Upland cotton (Gossypium hirsutum)

Plant height served as one of model traits to analyse dynamic development. The objective of this research was to investigate quantitative trait loci (QTL) and dynamic QTL for plant height trait using an intraspecific recombinant inbred line (RIL) population and a constructed genetic map in Upland cotton (Gossypium hirsutum L.). Totally, 41 QTL and 23 conditional QTL controlling plant height were detected at two experimental environments, respectively. Four stable QTL were identified simultaneously in both environments. Some QTL identified at the early stage could not be detected at the final stage at plant maturity. Conditional QTL with different genetic effects were identified at certain stages, demonstrating that the expression of QTL had temporal characteristic during plant growth. Therefore, the study of dynamic QTL could unravel temporal genetic patterns controlling complex developmental quantitative traits.     

Inheritance of plant height in the dwarf mutant 'Enana' of safflower

The dwarf safflower mutant ‘Enana’ has been developed from the cultivar ‘Rancho’ by chemical mutagenesis. The objective of the present research was to study the inheritance of plant height in crosses between ‘Enana’ and ‘Rancho’. Plants of both lines were reciprocally crossed and the F₁, F₂ and F₃ generations were obtained. The evaluation of plant height in the F₂ generation suggested the presence of a single locus controlling this trait. This was confirmed after the evaluation of 164 F_2:3 lines, which revealed an F₂ segregation fitting a 1:2:1 (dwarf: intermediate: standard) ratio. The locus was designated D^w. As the mutated allele was partly dominant over the wild‐type allele, the proposed genotype for ‘Rancho’ was d^w d^w, whereas that for ‘Enana’ was D^w D^w. Furthermore, a partial cytoplasmic effect on plant height was detected, with the heterozygote D^w d^w being about 6 cm taller when ‘Rancho’ was used as female.     

气象因子对北京地区不同秋眠等级苜蓿秋季刈割后再生高度的影响

为了研究气象因子对不同秋眠等级苜蓿秋后再生性能的影响,采用完全随机区组设计,研究了美国11个标准对照秋眠等级苜蓿品种秋季刈割后再生高度与气象因子的关系。结果表明：北京地区各秋眠等级的苜蓿在秋后刈割两周后再生高度便出现显著差异,各秋眠等级苜蓿植株再生高度的变化与三个气象因子的剩余效应较小,说明其他因子对苜蓿秋季刈割后植株再生高度的影响并不显著,因此可将积温、光照时数及降水量作为研究苜蓿秋眠性的主要影响因子。其影响程度依次为积温＞光照时数＞降水量。积温和光照时数对苜蓿秋季刈割后再生高度的影响最大。积温对再生高度的影响以直接效应为主,两者呈显著的正相关关系;光照时数和降水量均通过积温对再生高度产生正效应,而其对再生高度的直接影响为负效应。     

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn’t single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.     

Heterosis and combining ability for plant height and its components in hybrid wheat with Triticum timopheevi cytoplasm

The heterosis and combining ability for plant height and its components of hybrid wheat were investigated in an incomplete diallel experiment including 5 CMS lines and 4 restorer lines. The results showed that heterosis (HS) and heterobeltiosis (HBS) occurred in plant height (PH) and length of the first internode (LFI), second internode (LSI), third internode (LTI), basal internode (LBI) and the spike (LS) of hybrids, but their values varied among crosses and characters; the HS and HBS of LBI were larger than those of other characters, the HS and HBS of LSI and LTI contributed a lot to those of PH. There were significant relationships between internode lengths and PH for specific combining ability (SCA) and general combining ability (GCA), and among lengths of the adjacent internodes for SCA and/or GCA effects. However, the relationships of LS with the lengths of internodes and PH were insignificant for GCA, SCA, HS and HBS. The SCA effects were more important than GCA effects for LFI, the reverse was true for LSI, LTI, LS and PH, and the SCA effects was nearly equal to the GCA effects for LBI. So, LFI was mainly influenced by non-additive effect of genes, while LSI, LTI, LS and PH were mainly controlled by additive gene effects, LBI was controlled equally by additive and non-additive effects of genes. The genes that control the length of specific internode not only affect PH, but also the length of the adjacent internode. The genetic system in charge of lengths of internodes and plant height is independent of that for length of spike. Thus, it is possible to develop new wheat cultivars or hybrid combinations having long spike but dwarf plant height. This revised version was published online in July 2006 with corrections to the Cover Date.     

Soybean plant height QTL mapping and meta‐analysis for mining candidate genes

Plant height is closely related to seed yield of soybean. The goal of this study was to identify important loci affecting soybean plant height using meta‐analysis based on a reference physical map. Plant height related to QTLs was mapped across eight years with a RIL population by WinQTLCart v2.5. 182 QTLs related to plant height of soybean from database and our research were collected, and each QTL was projected onto the soybean physical map by software BioMercator v2.1. The confidence interval of meta‐QTL ranged from 0.09 to 5.07 Mb, and the mean phenotypic variance ranged from 4.9% to 73.0%. Furthermore, 4,259 candidate genes were located in these consensus QTLs, and 40 of them were involved in the plant growth and stem elongation and annotated as plant hormone signal transduction (pathway ID ko04075) in KEGG pathway. These results would lay a foundation for fine mapping of QTLs/genes related to plant height and marker‐assisted selection for breeding in soybean.     

Dynamic QTL mapping for plant height in the hybrid population of Agropyron Gaertn.

Plant height (PH) plays a very important role for plant breeding and also serves as a model trait to dynamic development study. The dynamic quantitative trait locus (QTL) analysis for PH of Agropyron Gaertn. was carried out in a cross-pollination (CP) hybrid population of A. Gaertn. based on the phenotypic data of PH at different developmental stages in four year-sites and the constructed single-nucleotide polymorphism (SNP) genetic map. The results showed that 69 QTL and nine major QTL were detected by unconditional QTL mapping. A total of 107 QTL and 13 major QTL were found using conditional QTL mapping. Forty-seven QTL were detected by two methods. Two unconditional QTL, Qph2-5 and Qph3-4, were expressed as major and stable QTL for PH. Four major stable conditional QTL for PH, cQph4-1, cQph4-8, cQph6-2 and cQph6-7, were detected. Two conditional PH QTL, cQph3-5 and cQPh3-7, were identified in four environments over multiple stages. The gene/QTL controlling PH was expressed in a certain spatiotemporal manner. These results could also provide a reference for genetic and breeding research of related plant.     

甘蓝型油菜茎高QTL定位及株高相关位点整合

甘蓝型油菜主茎高度(茎高)是株型的构成因子之一,研究其遗传机理对油菜株型改良具有重要的理论指导意义。目前对甘蓝型油菜茎高研究的报道较少。本研究以2个油菜茎高差异较大的亲本构建的重组自交系群体为材料,利用SNP高密度遗传图谱, 2年共检测到11个茎高QTL,分布在A04、A06、C04、A08和C01染色体上,位点的表型贡献率为7.25%～19.61%。同时,以455份来源不同的甘蓝型油菜为材料,结合重测序产生的SNP标记,对茎高进行全基因组关联分析, 2年共检测到5个SNP与茎高性状显著关联,分布在A08、A10、C02和C06染色体上。根据茎高定位结果,找到一些与激素途径(生长素、赤霉素和油菜素内酯)、光形态建成及植物生长发育相关的候选基因。在此基础上,结合国内外株高相关性状定位研究结果,将株高相关性状位点整合到甘蓝型油菜参考基因组上,发现4个以上群体都在A01、A03、A07、C03和C06染色体上找到株高定位的区间,2个群体在A10染色体上找到主花序长度共同定位的区间,在A02和C03染色体上找到一次分枝高度共同定位的区间。本研究中的茎高定位结果与整合后的株高相关性状QTL定位区间有部分重叠,位于A04、A06、A08、C04和C06染色体上。上述结果为甘蓝型油菜理想株型育种提供了理论依据。     

The reduced height genes do not affect the root penetration ability in wheat

Root penetration (RP) ability into compacted soil is an important breeding target for drought avoidance by durum (Triticum turgidum L. var. durum) and bread wheat (T. aestivum L.) in regions with compacted soils and water deficits. However, it is said generally that yield of the current cultivars introduced the reduced height gene (Rht-B1b or Rht-D1b) are more sensitive to drought stress than that of old landraces. This study investigated the effect of the Rht genes on RP ability using the seedlings of near-isogenic lines (NILs) of Rht genes of LD222 durum wheat and April Bearded bread wheat, and 110 recombinant inbred lines (RILs) of durum wheat derived from the cross between the tall landrace (Jennah Khetifa; Rht-B1a Rht-B1a) and semi-dwarf cultivar (Cham1; Rht-B1b Rht-B1b). One seedling of each genotype was grown in a pot (6 cm diameter, 15 cm height) with a disc of 3 mm thickness made from paraffin and Vaseline mixture (PV) in 10 cm depth, as a substitute for a compacted soil layer. The RP index [number of roots penetrating through the PV disc per plant (PVRN)/total number of seminal and crown roots per plant (TRN)] was measured at eight weeks after sowing and used as the indicator of RP ability of seedling. In NILs, the shoot length decreased significantly because of the introduction of either Rht-B1b or Rht-D1b dwarfing genes, but the RP index was similar to those of tall parents. In RILs, although the RP index and shoot length were higher in Jennah Khetifa than in Cham1, the relationship between RP index and shoot length was not significant (r = 0.156). Both results indicate that RP ability of wheat does not link to dwarfness regulated by Rht genes. We suppose therefore that it would be possible to develop a high yielding semi-dwarf cultivar with excellent RP ability.     

Genetic architecture of plant height in maize phenotype‐selected introgression families

This study aimed at developing, characterizing and evaluating two maize phenotypic‐selected introgression libraries for a collection of dominant plant height (PHT)‐increasing alleles by introgressing donor chromosome segments (DCS) from Germplasm Enhancement of Maize (GEM) accessions into elite inbred lines: PHB47 and PHZ51. Different backcross generations (BC₁‐BC₄) were developed and the tallest 23 phenotype‐selected introgression families (PIFs) from each introgression library (PHB47 or PHZ51) were selected for single nucleotide polymorphism genotyping to localize DCS underlying PHT. The result shows that most PIFs carrying DCS were significantly (α = 0.01) taller than the respective recurrent parent. In addition, they contained larger donor genome proportions than expected in the absence of selection or random mating across all BC generations. The DCS were distributed over the whole genome, indicating a complex genetic nature underlying PHT. We conclude that our PIFs are enriched for favourable PHT‐increasing alleles. These two libraries offer opportunities for future PHT gene isolation and allele characterization and for breeding purposes, such as novel cultivars for biofuel production.     

露天矿相邻采区间内排压帮高度及 重复剥离深度的综合优化

分析了不同压帮方式的内排运距特点与计算原理,建立了内排压帮高度及重复剥离深度的数学模型,得出通用的计算公式并给出有效判据。以黑岱沟露天矿为例,采用费用补偿法确定最优的内排压帮高度,利用最小重复剥采比确定最佳的重复剥离深度。研究结果表明：分区开采露天矿相邻采区间内排压帮高度与重复剥离深度需同时确定,以费用补偿法建立的数学模型简单且可靠,研究成果对露天矿相邻采区间生产设计具有指导意义。     

空间高度对球面网壳结构内爆炸响应的影响

基于修正后的Johnson-Cook材料模型,应用ANSYS/LS-DYNA建立K8型单层球面网壳计算模型,对内爆炸下不同空间高度的结构爆炸响应进行计算和分析。首先,分析结构内爆炸冲击波传播规律,验证模型参数选取的可行性;其次,讨论内爆炸作用下球面网壳的动力响应,对比分析不同本构模型对爆炸响应的影响;最后,定义下部支承结构所围体积占结构所围总体积的比值为空间高度系数,讨论空间高度系数对墙面未开洞和墙面开洞球面网壳动力响应的影响。结果表明,爆炸冲击波在球面网壳结构角部有汇聚效应,与反射冲击波共同作用,严重影响球面网壳结构的动力响应;对于墙面未开洞的球面网壳,爆炸响应受反射冲击波影响较大;对于墙面开洞的球面网壳,爆炸响应受空间高度系数影响较大。基于研究结果给出了球面网壳结构在内爆炸下防爆和抗爆设计的合理空间高度系数建议值。