Genetic dissection of vitamin E content in rice (Oryza sativa) grains using recombinant inbred lines derived from a cross between 'Zhenshan97B' and 'Nanyangzhan'

Vitamin E (VE) is an important nutritional trait in rice grains. In order to dissect the genetic basis underlying VE content, a recombinant inbred lines population derived from 'Zhenshan 97B' and 'Nanyangzhan' was used for quantitative trait locus (QTL) analysis. Totally, 29 QTLs for six VE traits were identified in 2 consecutive years. Among those, five QTLs repeatedly detected in two years formed a cluster on chromosome 2, which was responsible for all five VE isomers. OsγTMT, the gene encoding γ‐tocopherol methyltransferase in rice, was located to the same region and treated as the candidate gene. Sequence analysis of alleles from two parents revealed many polymorphisms, including 19 single nucleotide polymorphisms (SNPs) and two insert/deletions (Indels) in the promoter region, two nonsynonymous SNPs in exons, and 25 SNPs and an Indel in introns. Besides, a QTL for δ‐tocotrienol and two QTLs for α‐tocopherol were repeatedly detected on chromosome 5 and 8, respectively, all three regions carrying no homologous genes involved in VE biosynthesis. These results could be useful in development of rice lines displaying desirable VE content.     

Quantitative trait loci underlying soybean seed tocopherol content with main additive,epistatic and QTL × environment effects

Soybean (Glycine max [L.] Merrill) seeds are a major source of tocopherols (Toc), which could significantly improve immune system health of human and prevent or treat many serious diseases. Selection for higher Toc contents of seeds could increase nutritional value of soybean‐derived food, laying on an important breeding goal for many soybean breeders. The present objectives of the work were to evaluate various genetic effects of QTL associated with individual and total Toc content based on a RIL population (“Beifeng 9” × “Freeborn”) in six environments to improve the efficiency of molecular marker‐assisted selection (MAS) for high‐Toc breeding. The results described that eighteen, thirteen, eleven and thirteen QTL were associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc content, respectively, and have additive main effects (a) and/or additive × environment interaction effects (ae) in certain environments. Among them, four QTL for α‐Toc, two QTL for γ‐Toc, one QTL for δ‐Toc and four QTL for total Toc could increase α‐Toc, γ‐Toc, δ‐Toc and total Toc content via significant a effect, respectively, which have stronger stability in different years and locations. It implied a value for MAS. Additionally, twenty‐five, fifteen, eleven and twenty epistatic pairwise QTL associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc contents, respectively, were detected. The genetic information of the QTL effects obtained here would be beneficial for breeding soybean variety with high‐Toc content by MAS.     

Mapping quantitative trait loci (QTLs) underlying seed vitamin E content in soybean with main,epistatic and QTL × environment effects

Soybean (Glycine max (L.) Merr.) seed contains small amounts of tocopherol, a non‐enzymatic antioxidant known as lipid‐soluble vitamin E (VE). Dietary VE contributes to a decreased risk of chronic diseases in humans and has several beneficial effects on resistance to stress in plants, and increasing VE content is an important breeding goal for increasing the nutritional value of soybean. In this study, quantitative trait loci (QTLs) underlying VE content with main, epistatic and QTL × environment effects were identified in a population of F_5 : 6 recombinant inbred lines from a cross between ‘Hefeng 25’ (a low‐VE cultivar) and ‘OAC Bayfield’ (a high‐VE cultivar). A total of 18 QTLs were detected that showed additive main effects (a) and/or additive × environment interaction effects (ae) in different environments. Moreover, 19 epistatic pairs of QTLs were found to be associated with α‐tocopherol (α‐Toc), γ‐tocopherol (γ‐Toc), δ‐tocopherol (δ‐Toc) and total VE (TE) contents. The QTLs identified in multienvironments could provide more information about QTL by environment interactions and could be useful for the marker‐assistant selection of soybean cultivars with high seed VE contents.     

Identification of quantitative trait loci and candidate genes controlling the tocopherol synthesis pathway in soybean (Glycine max)

A recombinant inbred line (RIL) population was used to identify quantitative trait loci (QTLs) and their candidate genes controlling the tocopherol (Toc) synthesis pathway. The RIL population was cultivated in field conditions in 3 years. A genetic map constructed using 1624 DNA markers was used for QTL analysis. We identified 22 QTLs for seed tocopherol contents and their ratios, of which two QTL clusters on chromosomes (Chr) 9 and 14 exerted consistent large effects on tocopherol composition across the 3 years. The QTL cluster localized on Chr 9 might correspond to γ-TMT3, which controls the conversion of γ-Toc into α-Toc. The QTL cluster localized on Chr 14 was novel, which might regulate the conversion of MPBQ (a precursor of δ-Toc) into DMPBQ (the precursor of γ-Toc). The effect of the QTL cluster on Chr 14 was validated in a pair of near isogenic lines, and its candidate gene was mined. The identified QTLs and their candidate genes might be used in breeding programmes to improve α-Toc content in soybean seeds.     

大豆籽粒维生素E含量的QTL分析

维生素E(VE)具有提高人体免疫力、抗癌、预防心血管疾病等保健作用,从大豆中提取的VE安全性更高。本研究采用高效液相色谱技术(HPLC)检测大豆BIEX群体(Essex×ZDD2315)维生素E的α-生育酚、γ-生育酚和δ-生育酚含量。应用QTLNetwork 2.1软件分别检测到8个和12对控制大豆维生素E及组分含量的加性和互作QTL。α-生育酚含量加性和互作QTL累计贡献值分别为8.68%(2个)和15.57%(4对),γ-生育酚含量加性和互作QTL累计贡献值分别为8.59%(2个)和11.57%(2对),δ-生育酚含量加性和互作QTL累计贡献值分别为5.44%(1个)和17.61%(3对),维生素E总含量的加性和互作QTL累计贡献值分别为11.39%(3个)和9.48%(3对)。未检测到维生素E及组分含量和环境互作的QTL。未定位到的微效QTL累计贡献值为66.16%~75.32%,说明未定位到的微效基因的变异占2/3以上。各性状的遗传构成中,未检测出的微效QTL份额最大,加性QTL和互作QTL贡献相差不大。在育种中应考虑常规方法聚合微效QTL与标记辅助方法聚合主要QTL相结合。     

利用已测序水稻品种分析其农艺性状基因座

水稻重要农艺性状的基因定位研究在育种上具有重要意义。2004年在海南陵水县种植两个完全测序水稻品种日本晴与9311的F₂群体及双亲，分别考察了其单株分蘖数、穗数、有效分蘖数、穗长、主穗长、抽穗期、株高和剑叶8个农艺性状3次重复的平均值。用已构建的连锁遗传图谱（Nipponbare/9311-F₂遗传图谱）及Excel 2000和Mapmaker/QTL 1.1b软件对这8个性状间的相互关系和基因位点进行了分析。结果在LOD>2.0和P＜0.005的条件下共检测到41个QTLs，它们分布在水稻所有染色体上，单个QTL对性状表型贡献率11.0%～46.4%，其中大于20%的有22个。对选用已测序材料为亲本构建图谱来探讨水稻农艺性状的分子基础及其育种意义进行了讨论。     

QTL mapping for the tocopherols at milk stage of kernel development in sweet corn

Tocopherols have several beneficial effects in plants, and are indispensable micronutrients for humans. Sweet corn is a major source of tocopherols in high concentrations. In this investigation, tocopherol compounds in sweet corn were analyzed by high performance liquid chromatography. To detect quantitative trait loci (QTL) controlling accumulation of tocopherols at the milk stage in sweet corn, a F₂ population consisting of 229 F_2:3 lines was created from the cross between a high-total tocopherols line (A6) and a low-total tocopherols line (A57). A genetic map was constructed using 136 polymorphic molecular markers including one gene-targeted marker based on the tocopherol biosynthesis pathway (HPPD). Eleven putative QTLs for tocopherol content and composition were detected by composite interval mapping and located on Chr. 1, Chr. 2, Chr. 5, Chr. 6 and Chr. 10. Phenotypic variance explained by each QTL ranged from 4.74 to 41.16 %. Eight mapped QTLs were co-localized, suggesting that the same QTL affected the amounts of more than one tocopherol compound. One candidate gene-targeted marker (HPPD) showed co-localization with the major QTL for γ-tocopherol and total tocopherols. Only one interval (umc1177–bnlg1429) on chromosome one exhibited a QTL for α, δ, γ, and total tocopherols with high LOD and R² values. The primary conclusion of this work is that two major QTLs located on Chr. 1 and Chr. 5 can be used for improvement of sweet corn nutrition quality by marker-assisted selection.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Mapping of QTL controlling tocopherol content in winter oilseed rape

Tocopherols are natural antioxidants in vegetable oils and are important dietary nutrients. Enhanced tocopherol content has become an important objective in oilseed rape breeding. A segregating DH population was tested for 2 years at two locations in replicated field trials. Genotypic differences occurred for α‐, γ‐ and total tocopherol content as well as α/γ‐tocopherol ratio, but highly significant genotype x environment interactions resulted in low heritabilities. Using a mixed‐model composite interval mapping approach between one and five QTL with additive and/or additive x environment interaction effects could be mapped for α‐, γ‐ and total tocopherol content and α/β‐tocopherol ratio. In addition, one to six locus pairs with epistatic interaction effects were identified, indicating a strong contribution of epistasis to trait variation. In total, the additive and epistatic effects explained between 28% (α‐tocopherol content) and 73% (total tocopherol content) of the genotypic variance in the population, with individual QTL and locus pairs contributing between 7.5 and 29.2% of variance. Considering the low heritabilities of the tocopherol traits, the results of this study indicate that marker‐assisted selection may be an efficient strategy in a breeding program for enhanced tocopherol content in rapeseed.     

Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers

Grain size is a main component of rice appearance quality. In this study, we performed the SSR mapping of quantitative trait loci (QTLs) controlling grain size (grain length and breadth) and shape (length/breadth ratio) using an F₂ population of a cross between two Iranian cultivars, Domsephid and Gerdeh, comprising of 192 individuals. A linkage map with 88 markers was constructed, which covered 1367.9 cM of the rice genome with an average distance of 18 cM between markers. Interval mapping procedure was used to identify the QTLs controlling three grain traits, and QTLs detected were further confirmed using composite interval mapping. A total of 11 intervals carrying 18 QTLs for three traits were identifed, that included five QTLs for grain length, seven QTLs for grain breadth, and six QTLs for grain shape. A major QTL for grain length was detected on chromosome 3, that explained 19.3% of the phenotypic variation. Two major QTLs for grain breadth were mapped on chromosomes 3 and 8, which explained 34.1% and 20% of the phenotypic variation, respectively. Another two major QTLs were identified for grain shape on chromosomes 3 and 8, which accounted for 27.1% and 20.5% of the phenotypic variance, respectively. The two QTLs that were mapped for grain shape coincided with the major QTLs detected for grain length and grain breadth. Intrestingly, gs2 QTL specific to grain shape was detected on chromosome 2 that explained 15% of the phenotypic variation.     

越冬栽培稻产量性状相关QTL定位

越冬栽培稻是一类能越过自然冷冬季节并在第2年春季萌芽、正常开花结实、收获稻谷的水稻品种。本文通过对越冬栽培稻产量性状QTL分析,明确产量相关性状的遗传规律,旨在进一步解析越冬栽培稻产量性状的遗传机制,为育种创新利用提供理论依据。以3份越冬栽培稻构建的3个半同胞F2群体为材料。各考察15个产量相关性状,利用Excel 2003、GraphPad Prism 5.0和QTL IciMapping 4.10软件分析数据、绘制遗传图谱、定位QTL和联合分析。结果表明,产量性状表型值在3群体中呈连续正态分布,表现为数量性状遗传。共检测到37个QTL和26对上位性QTL,贡献率分别介于2.32%～36.31%和1.04%～2.05%;检测到9个同时影响2个及以上产量性状(一因多效)QTL标记区间;以联合分析检测到13个产量性状相关QTL,其中4个QTL区间与单群体检测QTL区间重叠;越冬栽培稻产量相关性状QTL以加–显性效应遗传为主、上位性遗传效应为辅。本研究将为越冬栽培稻产量相关基因挖掘及育种创新利用奠定基础。     

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.     

水稻中胚轴长度QTL分析

为分析水稻中胚轴伸长与赤霉素的关系及其遗传基础,以沈农265(长中胚轴)和丽江新团黑谷(短中胚轴)的RIL群体为材料,结合其连锁图谱,对水和赤霉素溶液两种培养条件下的中胚轴长度进行QTL定位。结果表明,浓度为1.50μmolL~(-1)的赤霉素可显著促进中胚轴的伸长。两种培养条件下,共检测到控制中胚轴长度的5个QTL,分布在第1、第2、第3、第6和第11号染色体上,LOD值在3.65～15.52范围内,单个QTL对表型贡献率在7%～33%之间。其中qML3、qML6和qML11在2种处理条件下均被检测到,qML1和qML2仅在水培条件下被检测到。与其他研究比较发现,主效基因qML3可以在不同群体和不同环境下稳定表达。     

Molecular mapping of soybean seed tocopherols in the cross ‘OAC Bayfield’ × ‘OAC Shire’

Soybean (Glycine max [L.] Merr.) is cultivated primarily for its protein and oil in the seed. In addition, soybean seeds contain nutraceutical compounds such as tocopherols (vitamin E), which are powerful antioxidants with health benefits. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) that affect accumulation of soybean seed tocopherols. A recombinant inbred line (RIL) population derived from the cross ‘OAC Bayfield’ × ‘OAC Shire’ was grown in three locations over 2 years. A total of 151 SSR markers were polymorphic of which a one‐way analysis of variance identified 42 markers whereas composite interval mapping identified 26 markers linked to tocopherol QTL across 17 chromosomes. Individual QTL explained from 7% to 42% of the total phenotypic variation. Significant two‐locus epistatic interactions were identified for a total of 122 combinations in 2009 and 152 in 2010. The multiple‐locus models explained 18.4–72.2% of the total phenotypic variation. The reported QTL may be used in marker‐assisted selection (MAS) to develop high tocopherol soybean cultivars.     

基于侯选基因标记的四倍体马铃薯休眠QTL关联分析

休眠期是马铃薯(SolanumtuberosumL.)重要的块茎性状之一,寻找调控马铃薯块茎休眠的关键基因,揭示其分子机制以选育具有适宜休眠期长度的马铃薯品种,对于解决当前马铃薯产业中过长或过短休眠期带来的经济损失和食品安全隐患等问题十分关键。前期研究在二倍体马铃薯连锁群体中定位了6个加性休眠QTL,本研究拟在四倍体马铃薯育种材料中验证这些休眠QTL。基于休眠QTL连锁的候选基因标记,采用混合线性模型(MLM),模型中考虑群体结构和亲缘关系(Q+K),在四倍体马铃薯自然群体St-hzau中对马铃薯块茎休眠期进行了关联分析。5号染色体上休眠QTL DorB5.3连锁的候选基因标记S199_300和GWD (根据葡聚糖水双激酶α-glucan water dikinase基因设计)与马铃薯块茎休眠期具有显著的关联(P0.05),分别解释了休眠期表型变异的7.8%和3.2%,分别能增加休眠期7.1 d和4.5 d,即在二倍体马铃薯连锁群体中定位的稳定主效休眠QTL DorB5.3在四倍体马铃薯关联群体St-hzau中也表现显著, DorB5.3的稳定性在关联分析结果中得到了验证,表明候选基因标记策略在马铃薯块茎休眠QTL关联分析中是一种有效的策略。本研究所验证的主效休眠QTL DorB5.3及相应连锁标记可以直接用于马铃薯休眠育种。据此可以推测GWD可能在控制还原糖含量和块茎休眠2个方面均发挥作用,马铃薯块茎休眠机制与还原糖含量变化机制可能存在着部分交叉。     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

甜玉米果皮厚度QTL的定位及上位性互作

果皮厚度是影响甜玉米口感的一个重要因素。发掘果皮厚度的基因资源、了解玉米果皮厚度的遗传机制,是指导其育种的基础。本研究以日超-1(薄果皮,56.57μm)×1021(厚果皮,100.23μm)的190个BC1F2家系为作图群体,分别采用2种遗传模型检测QTL。基于复合区间作图(CIM)共检测到3个影响果皮厚度的QTL,位于3.01、6.01、8.05区段,分别解释8.6%、16.0%和7.2%的表型变异,其中3.01和8.05处QTL以加性效应为主;基于混合线性CIM模型(MCIM)共检测到5个影响果皮厚度的QTL,其中除8.05处QTL为加性QTL外,另有2对加×加上位性互作QTL,1对是2.01和6.05处QTL之间的互作,另1对则是5.06和6.01处QTL间的互作。这2对互作QTL分别解释了6.63%和12.48%的表型变异率。本结果表明,加性效应和上位性互作效应等都在果皮厚度的形成和遗传中起重要作用。能够检测QTL上位互作的MCIM模型更适用于果皮厚度QTL定位。本研究还在其中4个QTL的区域内分别检索到胚乳中色素合成以及细胞转变的相关候选基因,这些基因的表达是否与果皮厚度的变异有关值得进一步研究。     

用(培矮64s/Nipponbare)F2群体对水稻产量构成性状的QTL定位分析

用水稻测序品种培矮64s和Nipponbare为亲本构建的含137个SSRs标记的连锁遗传图谱和(培矮64s/Nipponbare)F2群体的180个单株,对水稻的单株有效穗数、穗粒数、穗实粒数、结实率、穗着粒密度、千粒重等6个产量构成性状进行了QTL定位分析.共检测到6个性状的22个QTLs,分布在第1、2、4、5、6、9、10、11、12等9条染色体的14个区域,表型贡献率5.0%～19.3%;相关性较强的性状之间具有较多共同或紧密连锁的QTLs;集中分布的QTLs之间既有同向连锁,也有反向连锁.对不同水稻群体定位的同源QTL进行了比较,对QTL在染色体上的集中分布,以及用QTL定位结果和生物信息学方法相结合预测基因的功能等进行了探讨.     

利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

以东乡普通野生稻和日本晴为亲本构建的染色体片段置换系为研究材料,2019年分别在北京、山东临沂和江西南昌对分蘖数、穗粒数和粒形等11个产量相关性状进行多环境鉴定,结合染色体片段置换系基因型数据定位水稻产量相关性状QTL。3个环境共检测到68个QTL,包括株高4个、穗长5个、分蘖数2个、一次枝梗数7个、一次枝梗粒数8个、二次枝梗数8个、二次枝梗粒数10个、每穗粒数6个、千粒重7个、粒长8个和粒宽3个;LOD值介于2.50~12.66之间,贡献率变幅为4.67%~27.79%,15个QTL的贡献率大于15%;24个QTL与已报道位点/基因位置重叠,44个QTL为新发现位点;6个QTL在2个环境能被检测到,1个QTL qTGW2能在3个环境检测到,且是还未报道的新位点。最后,利用BSA法验证了qPH7、qPBPP8-2和qGW10三个QTL的可靠性。本研究将为后续产量相关性状基因克隆以及进一步解析其遗传基础和分子调控机制奠定基础。     

水稻粒型和粒重的QTL定位分析

利用以两个籼稻品种H359和Acc8558为亲本杂交建立的重组自交系群体及相应的分子标记连锁图，对水稻粒长、粒宽和粒重进行了QTL定位分析。检测到15个与粒长有关的QTL、17个与粒宽有关的QTL及16个与粒重有关的QTL，它们可分别解释75．91％、76．20％和81．40％的表型变异。其中在5号染色体上检测到1个控制粒宽的主效QTL，可解释26．65％的表型变异。粒长和粒宽之间虽然相关显著，但相关系数很小(r=0．180)。而QTL分析结果也显示，两者的QTL位置很少相同。这说明粒长和粒宽有不同的遗传基础。粒长和粒宽与粒重的相关系数分别为0．781和0．461，直接通径系数分别为0．7220和0．3299。QTL定位结果也显示，粒长与粒重的QTL位置相近或重叠的较多。因此，粒长对粒重的贡献较大。