Mining Applicable Elite Alleles of Growth Duration, Plant Height and Panicle Number per Plant by Conditional QTL Mapping in Japonica Rice

Unconditional and conditional QTL mapping were conducted for growth duration (GD), plant height (PH) and effective panicle number per plant (PN) using a recombinant inbred line (RIL) population derived from a cross between two japonica rice varieties Xiushui 79 and C Bao. The RIL population consisted of 254 lines was planted in two environments, Nanjing and Sihong, Jiangsu Province, China. Results showed that additive effects were major in all of QTLs for GD, PH and PN detected by the two methods, and the epistatic effects explained a small proportion of phenotypic variation. No interactions were detected between additive QTL and environment, and between epistatic QTL pairs and environment. After growth duration was adjusted to an identical level, RM80-160bp was detected as an applicable elite allele for PN, with an additive effect of 0.71. When effective panicle number per plant was adjusted to an identical level, RM448-240bp was detected as an applicable elite allele for GD, with an additive effect of 4.64. After plant height was adjusted to an identical level, RM80-160bp was detected as an applicable elite allele for PN, with an additive effect of 0.62, and RM448-240bp was detected as an applicable elite allele for GD, with an additive effect of 3.89. These applicable elite alleles could be used to improve target traits without influencing the other two traits.

Quantitative trait locus mapping of yield and plant height in autotetraploid alfalfa(Medicago sativa L.)

Alfalfa(Medicago sativa L.)is the most widely grown forage legume crop worldwide.Yield and plant height are important agronomic traits influenced by genetic and environmental factors.The objective of this study was to identify quantitative trait loci(QTL)and molecular markers associated with alfalfa yield and plant height.To understand the genetic basis of these traits,a full-sib F1 population composed of 392 individuals was developed by crossing a low-yielding precocious alfalfa genotype(male parent)with a high-yielding latematuring alfalfa cultivar(female parent).The linkage maps were constructed with 3818 single-nucleotide polymorphism(SNP)markers on 64 linkage groups.QTL for yield and plant height were mapped using phenotypic data for three years.Sixteen QTL associated with yield and plant height were identified on chromosomes 1 to 8.Six QTL explained more than 10%of phenotypic variation,representing major loci controlling yield and plant height.One locus on chromosome 1 controlling yield traits had not been identified in previous studies.Three QTL co-located with other QTL(qyield-1 and qheight-7,qheight-5 and qyield-4,qheight-6,and qyield-6).With further validation,the markers closely linked with these QTL may be used for marker-assisted selection in breeding new alfalfa varieties with high yield.

QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines(RILs) and their bi-parents, Zhonghuang 13(ZH) and Zhongpin 03-5373(ZP). The total genetic distance of this bin map was 3 139.15 cM,with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci(qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56-32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

Mapping and Comparative Analysis of QTL for Rice Plant Height Based on Different Sample Sizes within a Single Line in RIL Population

To clarify the most appropriate sample size for obtaining phenotypic data for a single line,we investigated the main-effect QTL(M-QTL) of a quantitative trait plant height(ph) in a recombinant inbred line(RIL) population of rice(derived from the cross between Xieqingzao B and Zhonghui 9308) using five individual plants in 2006 and 2009.Twenty-six ph phenotypic datasets from the completely random combinations of 2,3,4,and 5 plants in a single line,and five ph phenotypic datasets from five individual plants were used to detect the QTLs.Fifteen M-QTLs were detected by 1 to 31 datasets.Of these,qph7a was detected repeatedly by all the 31 ph datasets in 2006 and explained 11.67% to 23.93% of phenotypic variation;qph3 was detected repeatedly by all the 31 datasets and explained 5.21% to 7.93% and 11.51% to 24.46% of phenotypic variance in 2006 and 2009,respectively.The results indicate that the M-QTL for a quantitative trait could be detected repeatedly by the phenotypic values from 5 individual plants and 26 sets of completely random combinations of phenotypic data within a single line in an RIL population under different environments.The sample size for a single line of the RIL population did not affect the efficiency for identification of stably expressed M-QTLs.

Discovering forest height changes based on spaceborne lidar data of ICESat-1 in 2005 and ICESat-2 in 2019:a case study in the Beijing-Tianjin-Hebei region of China

Background:The assessment of change in forest ecosystems,especially the change of canopy heights,is essential for improving global carbon estimates and understanding effects of climate change.Spaceborne lidar systems provide a unique opportunity to monitor changes in the vertical structure of forests.NASA’s Ice,Cloud and Land Elevation Satellites,ICESat-1 for the period 2003 to 2009,and ICESat-2(available since 2018),have collected elevation data over the Earth’s surface with a time interval of 10 years.In this study,we tried to discover forest canopy changes by utilizing the global forest canopy height map of 2005(complete global coverage with 1 km resolution)derived from ICESat-1 data and the ATL08 land and vegetation products of 2019(sampling footprints with 17 m diameter)from ICESat-2.Results:Our study revealed a significant increase in forest canopy heights of China’s Beijing-Tianjin-Hebei region.Evaluations of unchanging areas for data consistency of two products show that the bias values decreased significantly from line-transect-level(−8.0 to 6.2 m)to site-level(^(−1).5 to 1.1 m),while RMSE values are still relatively high(6.1 to 15.2 m,10.2 to 12.0 m).Additionally,58%of ATL08 data are located in‘0m’pixels with an average height of 7.9 m,which are likely to reflect the ambitious tree planting programs in China.Conclusions:Our study shows that it is possible,with proper calibrations,to use ICESat-1 and-2 products to detect forest canopy height changes in a regional context.We expect that the approach presented in this study is potentially suitable to derive a fine-scale map of global forest change.

Analysis of unmanned aerial vehicle navigation and height control system based on GPS

According to the characteristic of global positioning system（GPS） reflection signals,a GPS delay mapping receiver system scheme is put forward,which not only satisfies the unmanned aerial vehicle（UAV） guidance localization but also realizes height measurement.A code delay algorithm is put forward,which processes the direct and land reflected signal and outputs the navigation data and specular point.The GPS terrain reflected echo signal mathematical equation is inferred.The reflecting signal area,when the GPS signal passes the land,is analyzed.The height survey model reflected land surface characteristic is established.A simulation system which carries guidance localization of the UAV and the height measuring control through the GPS direct signal and the land reflected signal is designed,taken the GPS satellite as the illumination source,the receiver is put on the UAV.Then the UAV guidance signal,the GPS reflection signal and receiver＇s parallel processing are realized.The parallel processing reduces UAV＇s payload and raises system＇s operating efficiency.The simulation results confirms the validity of the model and also provides the basis for the UAV＇s optimization design.

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration （GD） and productive panicle number per plant （PN） were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height （PH） in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat （SSR） marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

The Validity of Open-Source Elevations for Different Topographic Map Scales and Geomatics Applications

This paper presents an analysis of four open-source Global Digital Elevation Models (GDEMs) and compares them on two topographic profiles (nearly flat, and hills regions) for mapping and geomatics applications. The chief intention is to investigate if GDEMs-based heights, contour intervals, slopes, and topographic profiles are valid for all map scales of topographic mapping, which constitutes a major issue in mapping activities. Two case studies, the Nile delta in Egypt and Makkah city in Saudi Arabia, have been utilized to represent flat and moderate-topography patterns. The investigated GDEMs include the most-recent released models: ASTER v.3, ACE 2, SRTMGL1 v.3, and NASADEM_HGT v.1 released in 2019 and 2020 with spatial resolutions of 1 and 3 arc seconds. Available accurate Ground Control Points (GCP) consist of 540 stations in the Nile delta and 175 stations in Makkah. Based on the available datasets in two study areas, it has been found that the accuracy of investigated GDEMs over known checkpoints ranges from ±2.5 and ±5.1 meters in the Nile delta region, while it varies between ±5.1 and ±8.0 meters in the Makkah area. That indicates that the utilization of GDEMs in topographic mapping differs significantly between flat and hilly spatial regions. Therefore, it is recommended to avoid using GDEMs for developing topographic maps of scale 1:25,000 or larger in flat regions and map scale 1:50,000 or larger in hilly regions. Additionally, the accomplished results showed that all GDEM-based slopes do not match with the actual slopes from known GCP over cross section’s length up to 30 kilometers. Thus, it is concluded that GDEMs are not the appropriate heights’ source for topographic mapping at medium and large map scales, and could not be utilized for topographic profiling in precise engineering and geomatics applications.

湖南省似大地水准面模型对比研究

正常高系统是以似大地水准面为基准的高程系统,也是中国目前采用的高程系统。随着GNSS定位技术的广泛应用,已能在10-7~10-9的精度量级上获得测量点的平面位置,但是却一直未能以相应的精度求解点的高程值。因此,通过建立高精度、高分辨率的区域似大地水准面模型提升高程测量的精度,成为重要的技术手段。该文通过对湖南省2007似大地水准面模型后期各似大地水准面模型的对比研究,找到模型的差异,并对差异较大的地区进行特征分析,查找形成差异的原因,可为全省二、三等水准网测量和大地水准面再精化工作提供参考。

基于InDel标记的谷子株高QTL定位

插入/缺失(InDel)标记在植物基因组中广泛分布,然而谷子中InDel标记的数量十分有限。为挖掘InDel位点和开发分子标记,本研究基于衡谷12号和长农35号的深度重测序结果,分析其单核苷酸多态性(SNP)、InDel和结构变异(SV)。利用JoinMap 4软件构建连锁遗传图谱,利用WinQTLCart 2.5软件定位株高数量性状位点(QTL),利用生物信息学、测序和实时荧光定量PCR(qRT-PCR)进行候选基因分析。研究表明,3种变异类型数量由多到少排序为SNP>InDel>SV;获得1392个在衡谷12号和长农35号中具有多态性的InDel标记,多态性率为35.14%,这些标记在谷子9条染色体上分布不均;获得一张包含467个InDel标记的谷子遗传连锁图谱,该图谱总图距448.45 cM,平均图距0.96 cM;利用F2群体定位了4个株高QTL(qPH5-1、qPH5-2、qPH9-1和qPH9-2),进一步利用重组自交系(RIL)群体对其中2个效应值较大的QTL(qPH5-1和qPH9-2)进行验证,结果重新检测到qPH9-2,似然比的自然对数(LOD)值为93.6,加性效应为-46.15,解释表型贡献率(PVE)达91.06%;Seita.9G080400在编码区存在2处非同义突变,且在茎中表达水平呈极显著差异,推测Seita.9G080400可能是控制株高的关键候选基因。本研究开发的InDel标记能够良好地应用于株高QTL定位,同时可为谷子种质资源鉴定、亲缘关系分析等研究提供一套好用的分子标记。

控制玉米株高基因PHR1的基因克隆

株高属于玉米理想株型育种的一个重要指标,不但影响玉米机械化收获,更与玉米的倒伏性和生物产量密切相关。本研究以低剂量快中子(4.19 Gy)辐照诱变玉米自交系KWS39获得的矮秆低穗位突变体为研究对象,该突变体命名为plant height reducing mutant-1(phr-1),开展了表型性状的田间调查分析,并利用phr-1×B73获得的F2分离群体,借助极端性状混池测序分析法(BSA-seq)及目标区段重组交换鉴定的方法,基于B73参考基因组对目标区段内的基因进行挖掘和功能注释,定位候选基因。研究结果表明,在1号染色体Bin1.06区间可能存在变异位点,进而利用大的分离群体结合目标区段多态性标记开发,将目标区段精细定位分子标记到Umc1122和Umc1583a两个标记之间约600 kb区间,该区段内存在一个控制株高的已知基因Brachytic2(BR2),BR2编码一个调控玉米茎秆中生长素极性运输的糖蛋白。候选基因测序结果表明,phr-1是BR2基因在第4个外显子处插入了165 bp的序列,导致第547位氨基酸变为终止子,蛋白翻译提前终止。phr-1的基因突变位点和变异方式与已报道的br2-1单个碱基发生变异位点完全不同,通过等位杂交实验证明了phr-1突变体就是br2-1的一个新等位突变体,候选基因就是BR2基因。本研究为玉米BR2基因在玉米株高遗传改良中提供了新的种质资源。

展颖野生稻株高性状的遗传与SD1基因的等位变异分析

为了探究SSSL-B50和华粳籼74(HJX74)株高差异的原因,利用SSSL-B50与HJX74回交构建F2群体进行株高性状遗传分析与基因定位。结果显示,F1植株表现为高秆;260个单株组成的F2群体株高出现分离,高秆植株与半矮秆植株分离比例符合3∶1(χ^(2)=0.18<3.84),说明SSSL-B50高秆性状为显性性状,受1对显性等位基因控制。利用IciMapping软件对F2进行连锁分析,将SSSL-B50携带的高秆基因定位在1号染色体代换片段上的标记S18和X161之间38.38~39.07 Mb。候选基因筛选分析发现,定位区间内存在着“绿色革命”基因座位SD1。对展颖野生稻、SSSL-B50及HJX74进行SD1基因测序及序列比对,发现HJX74的CDS序列与展颖野生稻、SSSL-B50相比有280 bp的缺失,导致氨基酸编码提前终止。qRT-PCR结果表明,SD1表达量在SSSL-B50茎秆的第2,3,4节均显著高于HJX74。此外,与前人报道结果相比,展颖野生稻SD1基因编码的氨基酸序列发生了2处改变(E100G、Q339R)。研究结果弄清楚了展颖野生稻单片段代换系SSSL-B50高秆性状受SD1调控,同时从展颖野生稻鉴定到了SD1的新等位型SD1Glu。

融合星载GNSS-R数据和多变量参数全球海洋有效波高深度学习反演法

星载GNSS-R作为一种新兴的观测方法,最近被应用于有效波高反演。现有研究通常使用从延迟多普勒图中提取的特征值以构建经验地球物理模型函数反演SWH。然而,使用多个变量参数作为模型输入具有很大挑战。为此,本文提出了一个融合星载GNSS-R数据和多变量参数反演全球海面SWH的深度学习网络模型(GloWH-Net)。为了验证本文模型的性能,ERA5、WaveWatchⅢ和AVISO SWH数据被用作广泛测试的参考数据,以评估GloWH-Net模型和先前模型(即经验模型和机器学习模型)的SWH反演性能。结果表明,当分别使用ERA5、WaveWatchⅢ和AVISO SWH作为参考值时,所提的GloWH-Net模型反演SWH的均方根误差分别为0.330、0.393和0.433 m,相关系数分别为0.91、0.89和0.84。相比基于最小方差估计器的经验组合模型反演SWH的均方根误差分别降低了53.45%、48.06%和40.63%;相比袋装树机器学习模型反演SWH的均方根误差分别降低了21.92%、18.72%和4.47%。表明了本文方法在反演全球海面SWH方面具有显著优势。

大场景中基于IHDT的激光回环检测算法

针对大场景下机器人定位和地图构建中的累积漂移偏差问题,提出一种基于强度、高度与密度三进制模式(IHDT)描述子的激光回环检测算法。将点云空间划分为三进制单元块提取全局描述子IHDT,其中包含点云的强度、高度和密度信息。为提高回环检测的效率,避免直接匹配大场景中的关键帧,采用两阶段搜索算法;为确定与当前帧IHDT描述子最为相似的候选帧,通过检索历史帧IHDT的二进制矩阵,进而确定最终的目标回环索引。在KITTI 05大场景中,所提IHDT-LIO-SAM算法的轨迹均方根误差和标准差分别为1.81、2.23 m,相较于基于欧式距离的LIO-SAM回环检测算法分别减少34%和50%,显著降低了误差。在拥有多个回环的大场景中,所提方法展现出了更好的适应性。

利用野生稻单片段代换系鉴定株高性状QTL

【目的】株高是与水稻株型密切相关的农艺性状,对水稻产量具有重要影响。充分挖掘野生稻中优异株高遗传位点,可丰富栽培稻矮源基因,为培育理想株型水稻品种提供新的遗传资源。【方法】以南方野生稻(Oryzameridionalis)和短舌野生稻(Oryzabarthii)分别为供体亲本的两套单片段代换系群体(简称:MER-SSSLs和BAR-SSSLs)为材料,采用多年大田试验,测定多季株高表型,对两套SSSLs和受体亲本‘华粳籼74’(‘HJX74’)进行Duncan’s多重比较,分析SSSLs与‘HJX74’之间的差异显著性,检测控制株高性状的QTL。【结果】MER-SSSLs和BAR-SSSLs的株高在3个季节均呈单峰分布,群体内株系间株高表型变异范围分别为80.74~116.22 cm和80.26~167.33 cm。利用MER-SSSLs共鉴定到25个株高相关QTL,加性效应在-6.07~6.35cm,单个QTL解释的表型变异范围在2.34%~6.63%。其中7个QTL(qPHm2-1、qPHm2-2、qPHm3-1、qPHm4-2、qPHm5-1、qPHm5-4、qPHm5-5)在不同年份被重复鉴定到,表达稳定;且qPHm2-1、qPHm2-2、qPHm3-1、qPHm4-2、qPHm5-4未见报道,可能是来自南方野生稻控制株高性状的新QTL。利用BAR-SSSLs在2024年晚季共鉴定到21个株高QTL,加性效应范围在-5.41~29.28 cm,表型贡献率在2.45%~30.13%。其中qPHb1-4和qPHb10-1表型贡献率均大于18.00%,qPHb10-1可能是来自短舌野生稻控制株高表型的新QTL。【结论】水稻株高性状是由多基因控制的数量性状。利用MER-SSSLs鉴定到7个稳定的株高QTL,利用BAR-SSSLs鉴定到2个控制株高的主效QTL。该结果可为进一步克隆野生稻优异基因奠定基础,为水稻株高性状育种提供材料资源。

我国陆地区域似大地水准面对数字化测图的适用性分析

全球导航卫星系统(GNSS)与区域似大地水准面能够代替低等级水准测量,获取正常高成果。为服务于各省不同比例尺测图项目,本文分析我国陆地区域似大地水准面对数字化测图的适用性。首先,统计国内各省(市)的区域似大地水准面精度情况;然后,推导不同比例尺测图中,似大地水准面模型为满足不同地形类别下高程点的限差应达到的精度。结果表明,大多数省(市)的区域似大地水准面模型均优于±0.1 m,能够满足中大比例尺测图需要,可以为各省开展不同比例尺测图提供技术服务。

无人机技术在大面积建筑物高度测量中的应用

基于倾斜摄影测量原理,以天津市滨海新区某地区为研究区域,采用大疆公司Phantom 4 RTK无人机航摄系统获取测区影像数据,利用ContextCapture(Smart 3D)软件构建三维实体模型,并使用EPS软件进行模型空间信息的采集绘制工作,完成大比例尺地形图同时量取测区范围内所有房屋建筑物的高度。最后均匀选取部分点位与全站仪测量点位数据进行精度对比分析,得到平面点位误差均小于0.1 m,并计算出平面中误差为0.087 m,高度中误差为0.044 m,符合规范的要求,证明了技术的可行性。

基于天气雷达网三维拼图的混合反射率因子生成技术

首先基于1:25万的DEM(digital elevation model)数据、雷达站点信息、雷达波束高斯分布模式和标准大气情况下的波束传播路径计算了雷达的波束阻挡率,并把它与雷达实测的反射率因子分布情况进行比较,发现两者具有很好的定性一致性和很强的定量相关性;其次根据设置的波束阻挡率阈值和波束下限(波束底部越过地形的高度)阈值得到不受地形阻挡的最小扫描仰角在同一平面上的投影,即混合扫描仰角,这样计算出来的混合扫描仰角与雷达扫描方式无关,可用于不同扫描方式下的混合扫描反射率因子(没有波束阻挡的最低扫描仰角的反射率因子在同一平面上的投影)的获取;然后根据混合扫描仰角,利用标准大气情况下的雷达测高公式计算等射束高度,把来自雷达网中各雷达的等射束高度进行拼接得到等射束高度拼图,其中在各雷达重叠覆盖区,取最小的等射束高度;最后利用新一代天气雷达网三维拼图反射率因子数据以及等射束高度拼图数据得到天气雷达网的混合反射率因子,以便用于大范围降水估算算法中的降水率的计算。

利用不同群体对玉米株高和叶片夹角的QTL分析

应用H21×Mo17、自330×K36、B73×L050这3个F23∶群体为作图材料,利用SSR等分子标记,对株高、穗位高和叶片夹角3个性状进行了数量性状位点(QTL)分析。对株高共检测到18个QTL,对穗位高检测到12个QTL,对叶夹角检测到9个QTL。在这些影响不同性状的QTL中,有一部分处于染色体上的同一区域,有的则是区域间部分重叠或处于邻近区域。此外,有的QTL还与其他研究中发现的影响相应性状的质量性状基因位点处于相同基因组区域。

玉米株高和穗位高的QTL定位

用玉米自交系掖478和丹340构建了397个F2:3家系群体,利用双亲间多态的150个共显性SSR标记绘制分子连锁图谱,图谱总长度1478.7cM,标记间平均距离10.0cM。在5种环境下对株高和穗位高性状进行鉴定,复合区间作图法检测到21个株高QTL和25个穗位高QTL。于第1和5染色体的umc2025-umc1035及umc1822-bnlg1118区域检测到平均贡献率分别为12.2%和14.9%的株高QTL。于第3和5染色体的phi029-umc1102及phi109188-bnlg1118区域检测到平均贡献率达到10.2%和22.8%的穗位高QTL。第5染色体的Bin5.05-5.07区域可能存在控制株高和穗位高的主效QTL。株高和穗位高的基因作用方式主要是加性和部分显性效应。文章还分析了群体大小及试验环境对株高和穗位高QTL定位结果的影响。