The Identification of QTL Associated with Cotton Fruit Branch Length Suitable for Mechanized Harvest Utilizing BSA-seq

[Objective] This study aims to identify quantitative trait loci (QTLs) associated with cotton fruit branch length by using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) method. [Method] In this study, the cotton F₂ segregating population was developed with the short branch line Sujimian 125 and long-branch variety Sikang 1 as cross parents. According to the average internode length of fruit branches in middle, extreme individuals in F₂ population were divided into two groups to generate the bulked DNA samples. The whole-genome resequencing of two DNA bulks was applied to analyze the single nucleotide polymorphism (SNP) and insertion-deletion (InDel) between two groups, and the fruit branch internode length related QTLs were detected using Euclidean distance (ED). [Result] With SNP data obtained from sequencing, a 0.8 Mbp range associated region on chromosome A3 was identified; with InDel data obtained from sequencing, a 1.09 Mbp range associated region on chromosome A3 was identified. Two regions overlapped, and the overlapped range was 0.77 Mbp. [Conclusion] This result suggested that the difference between I-type fruit branch and zero-type was due to different genetic locus and pattern rather than dosage effect of the same gene.     

抗旱节水小麦分子遗传育种研究进展

干旱缺水等自然灾害会导致小麦产量年度间变幅较大,尤其在小麦主产区黄淮地区更为严重。小麦抗旱节水育种是应对干旱的重大措施。本综述对小麦抗旱节水常规育种、抗旱节水分子遗传育种相关性状QTL定位、抗旱相关功能基因克隆鉴定、转基因等方面的研究进展进行了综述。水旱亲本杂交与异地交叉选择是卓有成效的常规育种方法,通过分子标记鉴定了关于根重、根长、胚芽鞘、高水分利用效率等相关性状的大量QTL;42个抗旱相关基因被克隆并进行基因功能分析和验证,均从不同代谢通路上影响着小麦抗旱性;14个来自不同供体的抗旱相关基因被研究者导入小麦品种后,转基因小麦植株的抗旱能力均得到不同程度的提高,部分植株在产量和其它抗逆性方面也得到提高。以上研究进展为抗旱节水小麦分子设计育种提供了理论依据和发展方向。     

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。     

川麦42和川农16抗穗发芽QTL定位及聚合效应分析

【目的】小麦穗发芽严重影响小麦产量和品质,是全球小麦生产面临的重大问题之一。通过鉴定挖掘抗穗发芽QTL,聚合穗发芽抗性位点,选育抗穗发芽小麦品种,为四川小麦穗发芽抗性改良提供技术和材料支撑。【方法】以川麦42/川农16重组自交系（RIL,F₈）为材料,于2016—2018年分别在2个环境下对RIL群体进行籽粒发芽指数（GI,2016和2018）、籽粒发芽率（GR,2016和2018）和整穗发芽率（SGR,2017和2018）3个穗发芽指标测定。利用90K SNP芯片构建的遗传图谱检测全基因组穗发芽相关QTL,并分析抗性QTL聚合效应。【结果】双亲间GI、GR和SGR指标值差异显著,亲本川农16穗发芽抗性明显优于亲本川麦42。共检测到11个与穗发芽抗性有关的QTL,主要分布在2B、2D、3A、3D、4A、5A、5B和6B染色体上。5B染色体上检测到的单个环境表达的整穗发芽QTL解释的表型变异率最大,达到29%;在2D和3A染色体上检测到的整穗发芽主效QTL,以及5A染色体上检测到的与种子休眠相关的籽粒发芽主效QTL,在2个环境下均能表达,其抗穗发芽等位变异均来源于川农16。基因型分析发现,RIL群体中不同株系聚合抗性QTL的数量变幅为1—9个,表现为抗穗发芽的株系均携带4—9个与穗发芽相关的抗性QTL。重组自交系群体中6个株系GI、GR和SGR值均在15%以下,表现出高抗穗发芽特性;这6个优异株系聚合了多个与穗发芽相关的抗性QTL,且均聚合了川麦42在4A染色体上的微效QTL（QGi.saas-4A和QGr.saas-4A）,以及川农16在2D和5B染色体上的主效QTL（QSgr.saas-2D和QSgr.saas-5B）;编号为104和125的优异株系已通过审定,定名为川麦104和川麦64。其中,川麦104于2012年同时通过国家和四川省审定,其抗穗发芽能力强,产量、品质、抗病等优良性状突出,聚合了7个正向穗发芽QTL,包括2B、2D和5B染色体上来源于川农16的4个抗性QTL（QGi.saas-2B、QGr.saas-2B、QSgr.saas-2D和QSgr.saas-5B）,以及4A和6B染色体上来源于川麦42的3个QTL（QGi.saas-4A、QGr.saas-4A和QGr.saas-6B）;近年来,川麦104已成为西南麦区小麦育种的核心亲本,育成小麦品种（系）18个。【结论】共检测到11个抗穗发芽QTL,其中3个来源于川麦42,8个来源于川农16;RIL群体中的抗穗发芽株系均携带4—9个抗性QTL,优异株系川麦104和川麦64高抗穗发芽,均聚合了7个穗发芽抗性QTL。     

水稻黑条矮缩病抗性QTL定位

发掘水稻黑条矮缩病的抗性基因有助于抗病品种的选育,减少黑条矮缩病对水稻生产的危害。本研究构建了包含222个家系的L5494/IR36重组自交系群体。对该群体进行黑条矮缩病的田间诱发鉴定,抗性亲本IR36发病率为28.70%,感病亲本L5494发病率为84.26%,群体发病率范围为11.21%～89.81%。利用134对分子标记构建覆盖12条染色体的遗传连锁图谱,总遗传距离为1475.97 cM,平均标记间距为11.1 cM。利用QTL IciMapping 4.0对抗黑条矮缩病QTL进行分析,共检测到4个QTL,其中第1、第2、第9染色体上QTL的表型贡献率分别为12.64%、16.00%和8.43%,抗病等位基因来自抗病亲本IR36;第6染色体上QTL的表型贡献率为10.82%,抗病等位基因来自感病亲本L5494。在此基础上,利用93-11为供体、日本晴为背景的近等基因系材料,在qRBSDV-1定位区间内检测到来自93-11的抗性QTL。本研究结果为水稻黑条矮缩病抗性基因定位及分子标记辅助选择育种提供借鉴。     

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。     

利用重组自交系高密度遗传图谱定位水稻芽期耐冷QTL

为定位水稻芽期耐冷QTL,本实验以双季超级稻品种‘五丰优T025’的双亲‘五丰B’和‘昌恢T025’杂交衍生的重组自交系(recombinant inbred lines, RILs)群体为材料,对10℃低温处理的水稻幼芽的存活率、根数、根长和芽长进行了测定。利用QTL Icimapping v4.2软件,共检测到3个控制芽期耐冷性QTL：qRL1、qRL2和qBL6,分别位于第1、2、6染色体上,LOD值分别为2.98,2.51和5.26,分别解释表型变异的10.54%,8.67%和14.04%,其增效等位基因均来自于亲本‘昌恢T025’。这些QTL定位在6.75k~40.05 kb染色体区间,为后续利用这些QTL进行分子标记辅助,选育芽期耐冷籼稻新品种奠定了基础。此外,检测到13对影响水稻芽期耐冷上位性互作QTL,分布在所有12条染色体,其中第3染色体与第8染色体之间互作位点可解释的表型变异率达到21.77%,表明上位性互作QTL在调控水稻芽期耐冷过程中也发挥了重要作用。     

Genome wide association studies (GWAS) of element contents in grain with a special focus on zinc and iron in a world collection of barley (Hordeum vulgare L.)

Genome wide association studies (GWAS) were carried out to map Quantitative Trait Loci (QTL) associated with element contents in the grain using 336 spring barley. Of the elements analyzed, Fe content ranged from 21.9 to 91.0 mg kg⁻¹, Zn from 10.4 to 54.5 mg kg⁻¹, Ba from 0.2 to 8.9, Ca from 186.4 to 977.5, Cu from 1.5 to 9.8, K from 353.2 to 7721.5, Mg from 1049.8 to 2024.2, Mn from 8.1 to 22.9, Na from 55.9 to 627.9, P from 2272.9 to 5428.8, S from 880.7 to 1898.0, Si from 19.1 to 663.2, and Sr from 0.35 to 2.62 mg kg⁻¹. GWAS were carried out using 6519 SNP markers and multiple elements in MLM:PCA + K model in TASSEL software. Population analyses showed two sub-populations, primarily based on row types. GWAS for row types showed association with INTERMEDIUM-C, a modifier gene for lateral spikelet fertility in the 4H chromosome, validating current GWAS approach. GWAS also showed that 2 QTL for Ba, 2 for Ca, 4 for Cu, 11 for Fe, 2 for K, 3 for Mg, 6 for Mn, 4 for Na, 3 for S, 5 for Si, and 3 for Zn were mapped in barley chromosomes. The QTL identified in the current study are valuable for breeding nutrient dense barley cultivars in the future, especially Zn and Fe.     

春小麦抗旱耐热性QTL分析

为发掘控制小麦抗旱耐热基因位点,以小麦重组自交系(RILs)群体为材料,于2015-2017年小麦灌浆期进行干旱胁迫、热胁迫、旱热胁迫处理,并对抗旱耐热相关性状QTL进行分析。结果表明,在干旱胁迫、热胁迫、旱热胁迫下分别检测到22、36和30个QTL,其中控制旗叶叶绿素含量、旗叶含水量、穗粒重、千粒重的QTL数分别为26、21、22和19个。抗旱相关性状QTL位于2A、3B、4B、7B、3D、4D和7D染色体上,表型贡献率为9.38%～30.81%;耐热相关性状QTL位于2A、2B、3A、3B、4B、4D、5D、6D、7A和7B染色体上,表型贡献率为9.03%～34.97%。抗旱性共定位区间2个,分别位于2A(gwm294-wmc644)和7B(barc140-gwm297)染色体上;耐热性共定位区间2个,分别位于5D(cfd67-cfd40)和6D(barc196-barc54)染色体上;抗旱耐热性共定位区间3个,分别位于2A(gwm294-wmc644)、2B(wmc441-wmc317)和7B(wmc83-wmc276)染色体上,其中共定位区间gwm294-wmc644( Qcc-2A.2、 Qgw-2A.1)的贡献率超过10%,遗传距离较小(6.49 cM)。     

A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

We developed 178 recombinant inbred lines from a southern‐by‐spring oat population designated as “TxH.” These lines were genotyped to generate a high‐quality linkage map that resolved 6,902 markers into 21 linkage groups that matched closely with the latest hexaploid oat consensus map. Three major quantitative trait loci (QTLs) affecting heading date were found in locations that are consistent with known QTLs and candidate genes, and two other QTLs affecting heading date were found in novel locations. Five QTLs affecting plant height were found. Both sets of QTLs are responsible for transgressive segregation observed for these two traits. Four QTLs affecting resistance to crown rust, caused by the pathogen Puccinia coronata f. sp. avenae, were identified. Two of these QTLs are consistent with known clusters of rust resistance genes, while two may represent new locations of novel rust resistance genes. A complete set of SNP sequences suitable for generating markers for molecular selection is provided.