QTL Analysis of Rice Peduncle Vascular Bundle System and Panicle Traits

A double haploid (DH) population of rice (Oryza sativa L.) derived from anther culture of ZYQ8/JX17, a typical indica and japonica hybrid, was used for genetic analysis of rice peduncle vascular system and panicle traits. The number of large vascular bundles (LVB), the number of small vascular bundles (SVB) in the peduncle, and the panicle traits including the number of primary rachis branches (PRB), the number of spikelets per panicle (SNP), peduncle top diameter (PTD), and panicle length (PL) were investigated in the parents and DH lines. The quantitative trait loci (QTLs) for each trait were analyzed based on the constructed molecular linkage map of this population. Three QTLs for LVB (qLVB_1, qLVB_6 and qLVB_7) were detected on chromosomes 1, 6, and 7, respectively. Two putative QTLs for SVB (qSVB_4 and qSVB_6) were mapped on chromosomes 4 and 6 respectively. Four QTLs (qPRB_4a, qPRB_4b, qPRB_6 and qPRB_7) on chromosomes 4, 6, and 7, respectively, were detected for PRB. Three QTLs (qSPN_4a, qSPN_4b and qSPN_6) were identified on chromosomes 4 and 6, respectively, which could significantly affect SPN. Five QTLs for PTD (qPTD_2, qPTD_5, qPTD_6, qPTD_8 and qPTD_12) were identified on chromosomes 2, 5, 6, 8, and 12, respectively. Three QTLs for PL (qPL_4, qPL_6 and qPL_8) were detected on chromosomes 4, 6, and 8, respectively. Clustering of QTLs, such as qLVB_6, qSVB_6, qSNP_6, qPTD_6, and qPL_6 detected in the interval G122_G1314b on chromosome 6, was found. These results suggest that some QTLs for peduncle vascular bundle system are possibly responsible for the panicle traits.

Mapping QTLs for Panicle Traits Based on Rice RIL Population Derived from TD70 and Kasalath

Two hundred and forty recombinant inbred lines （RIL） derived from a cross TD70/Kasalath and its linkage map including 141 SSR markers were used to map QTLs controlling panicle length （PL）, total seeds per panicle （TSP） and grain density （GD） in 2010 and 2011. The results showed that a total of 23 QTLs controlling three panicle traits were detected on chromosomes 2, 3, 4, 6, 7, 8 and 10, respec- tively, including 5 QTLs controlling PL, 8 QTLs controlling TSP, 10 QTLs controlling GD, with the LOD value ranging between 2.5-9.3, and the QTLs explained the ob- served phenotypic by 4.0%-20.8%. The marker interval RM5699-RM424 on chro- mosome 2, RM489-RM1278 on chromosome 3, RM3367-RM1018 on chromosome 4, RM3343-RM412 on chromosome 6 were common marker intervals for TSP and GD; six QTLs （qPL3, qTSP4, qTSP6-2, qTSP7, qGD3-2 and qGDT） were detected in two years. Among these QTLs, the qPL3, qTSP6-2, qGD3-2 and qGD7 were major QTLs. All QTLs for PL mapped in the present study had been mapped QTLs previously by other research groups, 16 QTLs controlling TSP and GD were new ones which contributed the observed phenotypic variance range by 4%-9.5%. These results laid a founda^ion for further fine positioning or cloning these QTLs.

Combining Ability Analysis of Panicle Traits in Six CIMMYT Maize Inbred Lines

In this study, six CIMMYT maize inbred lines and five representative do- mestic maize inbred lines were used as parental lines. By using incomplete diallel cross design, 30 hybrid combinations were developed to analyze the general com- bining ability （GCA）, specific combining ability （SCA） and total combining ability （TCA） of seven panicle traits in six CIMMYT maize inbred lines. The results showed that CIMBL98 and GEMS13 were excellent inbred lines with good compre- hensive performance; CIMBL98 × 340 and GEMS13×Chang 7-2 were superior combinations.

Morphological and physiological traits of large-panicle rice varieties with high filled-grain percentage

financed by the Special Program of Super Rice of Ministry of Agriculture, China （02318802013231）;the National Public Services Sectors （Agricultural） Research Projects, Ministry of Agriculture, China （201303102）;the Great Technology Project of Ningbo, China （2013C11001）

Relationships of Panicle Type Index with Subspecies Characteristics and Yield Traits in Filial Generation of Crosses between Indica and Japonica Rice

Two recombinant inbred line （RIL） populations, one derived from a cross between Zhongyouzao 8 （indica） and Toyonishiki （japonica） and the other from a cross between Qishanzhan （indica） and Akihikari （japonica）, were grown in Liaoning and Sichuan Provinces, China, to study the panicle type index （PTI, the ratio of a number of node position on panicle axis where the secondary branch with the most numerous secondary branch grains is located to the number of primary branches） and its relationships with subspecies characteristics and yield traits. With continuous distribution of PTI and numerous of lines with different PTIs in the progenies, indica-japonica hybridization could be a method for breeding cultivars with ideal panicle type. PTI was significantly influenced by environments, with a significant decrease from Liaoning to Sichuan A significantly negative correlation was found between PTI and most of subspecies characteristics. PTI varied remarkably with different subspecies types. As a whole, it showed a trend of indica （H）〉indicalinous （H＇）〉japonicalinous （K＇）〉japonica （K） However, it is not appropriate to regard PTI as a parameter for subspecies classification in rice because it was recombined in the filial generations of cross between indica and japonica rice. The negative correlations were found between PTI and most of panicle characteristics, as well as yield-related traits. Based on PTI, most of lines from the two populations were middle dominant panicle type （the number of grains on the secondary branch is numerous in middle position of the panicle） and lower dominant panicle type （the number of grains on the secondary branch is numerous in lower position of the panicle and becomes less towards the top of panicle） with significant yield advantages.

Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles （as many as 30 or more） than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.

Genetic Dissection of Quantitative Trait Loci for Panicle Traits and Heat Tolerance by High-Density Bin Map in Rice

A recombinant inbred line(RIL)with 179 lines derived from a cross between a heat tolerant line Huhan 1B and a heat sensitive line Hanhui 3 was used for QTL mapping for panicle traits and heat tolerance.A total of 52 QTLs were identified with LOD scores from 3.85 to 54.93,each explaining 0.70%to 21.48%of the phenotypic variances,including 11 for panicle length(PL),11 for seed number per panicle(SN),14 for spikelet number per panicle(SNPP),6 for seed-setting rate(SSR)under normal conditions,and 5 for seed-setting rate(SSR_HT)and 5 for relative seed-setting rate(RSSR)under heat stress,respectively.

QTLs analysis of rice peduncle vascular bundle and panicle traits

The vascular bundle in plants plays an important role intransportation of photosynthetic products, mineral nutri-ents, water, arid so on. Significant positive correlationswere found between grain yield, panicle traits and the No.of peduncle vascular bundles. So, it is very important tostudy the inheritance of peduncle vascular bundle, whichis a quantitative trait.

New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments

Panicle angle （PA） of 254 recombinant inbred lines derived from a cross between two japonica varieties Xiushui 79 and C Bao was investigated under four environments,and a genetic linkage map including 111 SSR markers was constructed.Genetic analysis was conducted by mixed major gene plus polygene inheritance models,and quantitative trait loci （QTLs） identification by the QTLNetwork 2.0 and the composite interval mapping approach of WinQTLCart 2.5 software.Results showed that the PA trait was controlled by two major genes plus polygenes,mainly by major genes.Eight QTLs for PA were detected by the QTLNetwork 2.0 software,and each locus explained 0.01% to 39.89% of the phenotypic variation.Twelve QTLs for PA were detected by the WinQTLCart 2.5 software,with each locus explaining 2.83% to 30.60% of the phenotypic variation.Two major QTLs （qPA9.2 and qPA9.5） distributed between RM3700 and RM3600 and between RM5652 and RM410,respectively,and a moderate QTL （qPA9.7） distributed between RM257 and OSR28,were both detected by the two methods in all of the four environments.The negative effect alleles of the three QTLs were from Xiushui 79.In addition,eight pairs of epistatic QTLs with minor effects were also detected.QTL × environment interactions were not significant for additive QTLs and epistatic QTL pairs.

Effects of Aphelenchoides besseyi Infection on Yield Traits of Different Rice Varieties (Lines)

[Objective] This study aimed to reveal the effects of Aphelenchoides besseyi infection on different rice varieties（lines）.[Method] By field observation and indoor phenotypic investigation,four conventional japonica rice varieties（lines） and japonica rice restorer line R161 under natural onset conditions were observed and analyzed.[Result] After being infected by A.besseyi,different rice varieties（lines）exhibited various symptoms.Specifically,Ning 1707,Ning 1818,Zhendao 88 and Nanjing 9108 had withered leaf tips and exhibited the symptoms of ＂small grains and erect panicles＂;japonica rice restorer line R161 only had withered leaf tips without symptoms of ＂small grains and erect panicles＂,and the withering symptoms occurred in flag leaf tip,whole flag leaf and top second leaf,respectively.After being infected by A.besseyi,all the experimental materials could sprout normally,but their plant height,panicle length,seed-setting rate and 1 000-grain weight were affected to varying degrees.In addition,after being infected by A.besseyi,various symptomatic tissues of R161 exerted different effects on rice yield.Especially,panicles with withered and twisted whole flag leaf were most affected.[Conclusion] This study provided the basis for further exploration of the damages of A.besseyi infection to rice and development of corresponding control measures.

An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning

Rice panicle phenotyping is required in rice breeding for high yield and grain quality.To fully evaluate spikelet and kernel traits without threshing and hulling,using X-ray and RGB scanning,we developed an integrated rice panicle phenotyping system and a corresponding image analysis pipeline.We compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy(R~2 of 0.99)and speed.Faster R-CNN was also applied to indica and japonica classification and achieved 91%accuracy.The proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

粳稻穗型性状与谷粒性状的相关性研究

以247份粳稻品种为试材,分析了穗型性状与谷粒性状间的相关性。结果表明,8个性状变异系数在4.8%~31.2%,穗型性状、谷粒性状中各性状平均变异系数分别为22.2%、7.8%。粒型因子、粒重因子、粒数因子、结实因子、穗长因子是影响粳稻品种穗型性状和谷粒性状综合表现的主要因子。穗型性状、谷粒性状间存在复杂相关性。同时,粳稻直立穗型、半直立穗型、弯曲穗型品种具有不同的穗型性状和谷粒性状。

基于全基因组关联分析的水稻穗长QTL定位及其候选基因分析

分别于2021年和2022年在湖南长沙种植254份水稻3K种质资源,在成熟期测定各种质的穗长。结合种质基因型进行全基因组关联分析,共检测到3个穗长QTL,分布于水稻第1、5、6号染色体,分别命名为qPL-1、qPL-5和qPL-6,相对贡献率为9.06%~28.27%;结合QTL区间内基因功能注释和基因不同单倍型的穗长差异显著性分析结果,最终获得qPL-1、qPL-5和qPL-6的候选基因,其中qPL-6与sped1-D共定位,Os01g0715600、Os05g0132700为调控穗长的新候选基因;对Os01g0715600、Os05g0132700和Os06g0597500的单倍型进行聚合分析,发现这3个基因存在累加效应。

不同玉米品种产量及其构成因素差异分析

为深入探究施用液体配方肥条件下不同玉米品种产量的差异,本试验以MC670、农华101、农华5号和农华106为试验材料,对其产量及其构成因素进行分析。结果表明:农华5号表现最好,有效穗数最多、出苗率最高,分别为77820穗/hm2和98.50%,较其他品种增加1.33%~2.67%;籽粒含水量最低,为24.33%,较其他品种减少4.48%~11.20%;穗籽粒干重为199.00 g,较其他品种增加3.10%~12.61%;穗粒数为563粒,较农华101增加9.75%;百粒重为35.30 g,较其他品种增加2.38%~17.35%;产量最高,为15472.89 kg,较其他品种增加5.84%~14.59%。由此表明,农华5号可作为高产品种在当地推广种植。

水稻CSSL-Z481代换片段携带的穗部性状QTL分析及次级代换系培育

【背景】粮食安全是保障国家安全的重要基础,水稻是人民赖以生存的主要粮食作物,提高其产量是重要的育种目标。水稻产量由每株有效穗数、每穗实粒数和粒重等性状构成,其中,粒重与籽粒形状、充实程度等密切相关。但这些性状都是由多基因控制,遗传基础复杂。染色体片段代换系(CSSL)可将这些复杂性状的QTL较准确地分解为单个孟得尔因子研究,且与育种工作紧密衔接,因而是理想的遗传研究和育种材料。【目的】前期以4代换片段的水稻染色体片段代换系Z481精细定位了一个易落粒基因SH6,但Z481与受体日本晴间还存在多个显著差异的穗部性状。明晰控制这些差异性状的QTL在代换片段上如何分布,并分解为单片段代换系,对目标QTL的图位克隆及应用于水稻分子设计育种有重要应用价值。【方法】利用受体亲本日本晴与Z481杂交构建的次级F2分离群体以SAS9.3统计软件的混合线性模型(mixed linear model,MLM)法进行穗部性状QTL定位(P<0.05),然后,根据基因型和表型,从F2选择42个单株在F3株系利用MAS法培育单片段及双片段代换系,并利用IBM SPSS Statistics 25.0的ONE-WAY ANOVA和TWO-WAY ANOVA分析及LSD和Duncans多重比较(P<0.05)分析这些单片段代换系(SSSL)和双片段代换系(DSSL)的QTL加性和上位性效应。【结果】以日本晴/Z481构建的次级F2群体共定位出12个控制水稻穗部性状的QTL,并培育出相应QTL的11个单片段代换系(S1—S11)和3个双片段代换系(D1—D3)。其中,有8个QTL(qGL1、qGL3、qGL6、qGW1、qGW3、qRLW1、qRLW3和qRLW6)可被单片段代换系所验证,表明这些QTL遗传稳定。此外,利用单片段代换系鉴定到qGL1-2、qGL1-3、qGL3-2等33个QTL。其中,qNSB1-1等15个可能为新鉴定的QTL。且利用3个DSSL分析了非等位QTL间的上位性效应,结果表明,不同QTL聚合会产生不同的上位性效应,如qGL3(a=1.26)和qGL6-2(a=0.86)聚合产生了-0.77的上位性效应,据DSSL遗传模型,D2的粒长遗传效应(1.35)产生了更长的粒长表型;qGWT3-2(a=3.18)和qGWT6-2(a=3.39)聚合产生了-5.46的上位性效应,则D2的千粒重遗传效应(1.11)产生了更小的籽粒。【结论】Z481的4个代换片段上共携带45个水稻穗部性状的QTL,并进一步分解到11个次级单片段代换系上,单片段代换系具有比F2群体更高的QTL检测效率。利用SSSL和DSSL解析的水稻穗部性状QTL的加性效应和上位性效应,有助于根据这些遗传信息预测设计基因型的表型,从而选择合适的SSSL进行育种设计。

荆门地区节水耐旱水稻品种播期试验

荆门市属于亚热带季风气候,近年来,农业气象灾害特别是高温干旱天气频发,对水稻生产造成了一定的影响。本研究以节水耐旱水稻品种旱优3号、旱优116作为试验材料,研究不同播期对其生育期、穗粒性状、产量等的影响。结果表明:随着播期的推迟,两个品种全生育期相应缩短,结实率也相应下降;两个品种均为中穗型品种,着粒均较稠密,分蘖力均为中等;产量方面,旱优3号以5月24日播期处理最高(9247.5 kg/hm^(2)),旱优116以5月29日播期处理最高(9967.5 kg/hm^(2))。

基于高密度遗传图谱对高粱穗部性状的QTL定位

利用高密度遗传图谱进行高粱穗部相关性状的QTL分析,为酒用高粱标记辅助育种和重要基因遗传机制解析提供理论依据。以美国籽粒高粱品种BTx623和酱香型白酒用高粱品种红缨子构建的包含205个家系的RIL群体为试验材料,2020-2021年在贵州贵阳、安顺和海南乐东的5个环境下,开展了5个穗型性状(穗长、穗柄长、穗轴节数、一级枝梗数和最长一级枝梗长)的调查。利用高密度连锁图谱,采用完备区间作图法(ICIM)开展QTL定位。在高粱的基因组上一共检测到61个QTL涉及45个不同QTL遗传位点,其中与穗长、穗柄长、穗轴节数、一级枝梗数和最长一级枝梗长相关QTL分别为14、10、8、11和18个。在多个性状或多个环境中被重复检测到的19个重要QTL位点分别位于1(3个)、3(4个)、4(2个)、5(1个)、6(4个)、7(1个)、8(3个)和9(1个)号染色体上,并在其中12个QTL位点置信区间内或附近确定了13个候选基因,它们与控制水稻穗型的基因同源(DEP1、RGN1、OsPID、OsSPL7和WTG1等),为进一步克隆和功能验证这些候选基因提供依据。

三江源7个糙毛以礼草植物学形态及遗传多样性分析

通过对三江源地区的7份糙毛以礼草(Kengyilia hirsuta)穗部性状指标主成分分析、染色体组核型分析及标签-简单序列重复(EST-SSR)分子标记分析,旨在阐明糙毛以礼草种质的形态学差异及种质间遗传多样性,为牧草育种和麦类作物改良提供理论依据。结果表明:糙毛以礼草的不同穗部性状间的变异系数差异较大,其中桴毛的差异最大;在穗部大小及密度、小穗特征是引起差异的3个主成分,颖长、稃毛长、穗长、穗宽指标是造成糙毛以礼草形态性状差异的主要因素;海晏糙毛以礼草的种质内差异最大。7份糙毛以礼草种质均为六倍体,染色体数目为42条,中部着丝点染色体为主要染色体类型;在不同类型的着丝点染色体数目、有无随体上表现出了丰富的多态性;核型指标多样性丰富,其中贵德糙毛以礼草、海晏糙毛以礼草为2C型,其余种质均为2B型;共和糙毛以礼草进化程度最高,海晏糙毛以礼草次之,莫湘滩糙毛以礼草最低。在EST-SSR多样性分析中,海晏糙毛以礼草和刚察糙毛以礼草两个种质与其他种质遗传距离相对较远。

穗粒数基因Gn1a在直立穗粳稻品种中的遗传效应分析

Gn1a是控制穗粒数的重要基因,对提高水稻单产具有重要意义。利用Gn1a基因内功能标记Gn1a-M1对44份迟熟中粳品种进行检测,结果显示该基因尚未在直立穗迟熟中粳品种中得到应用。为探明Gn1a在直立穗粳稻中的遗传效应,构建一套以直立穗粳稻品种海丰1号(gn1agn1a)为受体亲本,籼稻黄华占(Gn1aGn1a)为供体亲本,包含133个系的导入系群体,并通过重测序明确其中39个导入系携带Gn1a基因。在此基础上,通过对10个携带Gn1a基因导入系、10个未携带Gn1a基因导入系以及受体亲本农艺、产量和品质性状的测定及分析,明确了Gn1a基因在直立穗粳稻背景下能显著增加二次枝梗数、二次枝梗颖花数、穗长及一次枝梗数,但显著降低单株穗数;在外观品质上表现为粒宽显著增加、长宽比显著减小,垩白粒率和垩白度有增加的趋势,但对稻米淀粉理化性质和蒸煮食味品质影响较小。

利用东乡野生稻染色体片段置换系鉴定穗部性状主效QTL

【目的】稻穗是水稻产量的主要承载者,发掘穗部性状相关的主效QTL对进一步精细定位、克隆和育种利用具有重要意义。【方法】以粳稻日本晴为受体、东乡野生稻为供体构建的一套染色体片段置换系(chromosome segment substitution lines,CSSLs)群体为材料,在4个生态环境下进行穗部性状表型鉴定与主效QTL定位分析。【结果】不同生态环境下CSSL群体穗部性状存在较大幅度变异,东乡野生稻染色体片段的导入显著改变背景亲本的穗部性状,具有明显的增产效应;早季、中季、晚季和海南环境下共检测到64个控制每穗颖花数和籽粒大小的QTL,其中qPL2、qSN1.2、qSN2、qFGN3、qTGW2、qTGW12.1和qSL2在3个环境下稳定表达,21个QTL在2个环境下被重复检测到,其余QTL仅在单一环境下被发现;主效QTLqSN1.1、qSN1.2、qSN2、qSN3和qSN12对每穗颖花数具有明显的影响,多个QTL聚合具有明显调控每穗颖花数的功能;主效QTLqSL2、qSL3.2、qSLW3.1、qSLW3.2、qTGW8.1和qSLW10对籽粒大小具有明显的影响。这些位点分别作用于粒长、粒宽和长宽比,相互作用、共同决定籽粒大小;同时,穗部性状QTL成簇分布于10个染色体区段,其中主效QTL簇qGNS1.1、qGNS1.3、qGNS2.1、qGNS3.1、qGNS9、qGNS10和qGNS12包含多个调控每穗颖花数及籽粒大小性状的QTL,可在不同环境下稳定表达。来自东乡野生稻的等位基因具有明显调控产量表型的功能。【结论】研究结果不仅为东乡野生稻优异基因发掘奠定基础,也可为水稻穗部性状的分子育种提供新基因源。