基于高密度Bin图谱的水稻抽穗期QTL定位

以粳稻品种02428和籼稻品种玉针香进行杂交, 按单粒传法连续自交10代, 得到包含192个株系的重组自交系(RIL)作图群体。通过对两亲本重测序及RIL群体简化基因组测序, 构建了包含2711个Bin标记的高密度遗传图谱。该图谱各染色体标记数在162~311个之间, 标记间平均物理距离为137.68 kb。将亲本及192个株系分别于4个环境下采用随机区组种植, 并记录抽穗期。使用WinQTL Cartographer 2.5软件的CIM分析方法, 进行抽穗期相关QTL检测及定位。在4个环境下定位到影响抽穗期的QTL共14个, 分布于第1、第2、第3、第7、第8、第9和第10染色体。其中, qHD2.2和qHD10.2能在3个环境中被重复检测到, 表型贡献率分别为5.14%~11.15%和5.35%~16.97%, 分别能缩短抽穗期1.66 d和1.56 d, 具有聚合育种的应用价值。通过物理位置比对, 14个QTL中有11个与前人定位在相同或邻近区域, qHD1.1、qHD2.2和qHD9.1尚未见报道。经对qHD2.2详细分析, 在其染色体区间内找到3个与抽穗期相关的注释基因LOC_Os02g46450、LOC_Os02g46710和LOC_Os02g46940, 其中LOC_Os02g46450已被克隆。测序分析发现, 这3个基因在两亲本间都存在差异, 可作为候选基因。     

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.)

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China.     

江苏不同熟期粳稻品种的齐穗期和安全播期预测

为明确当前江苏各地不同熟期粳稻品种的安全播期,以江苏的4个熟期类型的5个常规粳稻品种为材料,在江苏连云港(34°83′N)、淮安(33°34′N)、扬州(32°25′N)和苏州(31°18′N)等4地,进行自5月10日起每10天1期,共8个播期的播种试验,得出各播期的相应齐穗期。以齐穗期温光预测模型y=a＋b₁x₁＋b₂x₂拟合其实得的播期与齐穗期资料。用该模型拟合4个试验点、5个供试品种计20组数据,得出20个预测式,其拟合度R²在0.9927~0.9998之间,均达极显著水平。用各试点所在地近25年各年粳稻品种安全齐穗期及逐日平均温度,依齐穗期光温模型预测式经多次迭代推得各年的安全播期,进而求得90%保证率的安全播期并作各地生产应用分析。在江苏淮北的北部,麦稻两熟田水稻的可播栽始期为6月15日,中熟中粳的安全播期为6月21日,此类品种可用于该地直播;其他各熟期类型品种安全播期均早于当地可播栽始期,故不能用于直播。在淮北南部稻麦两熟田的可播栽始期为6月12日左右,中熟中粳和迟熟中粳的安全播期分别在7月4日和6月22日,此两类品种可用于该地麦茬直播;早熟晚粳安全播期在6月17日、18日,在大面积生产中因接茬时间过紧应慎用于麦茬直播;中熟晚粳的安全播期为6月8日,不可用于直播。在苏中南部,水稻可播栽始期为6月8至11日,中熟中粳、迟熟中粳、早熟晚粳类型两品种的安全播期分别在7月12日、3日、6月25日和28日,可用于该地直播;中熟晚粳的安全播期为6月11日,用于直播接茬时间太紧,不可应用。在苏南,水稻的可播栽始期为6月5日,供试4熟期类型品种的安全播期分别为7月18日、13日、9日至10日和7月3日,仅考虑安全齐穗各熟期类型品种均可用于麦茬直播,但因中粳类型品种直播稻生育期过短、产量不高,不宜应用。     

Mapping quantitative trait loci influencing panicle‐related traits from Chinese common wild rice (Oryza rufipogon) using introgression lines

Panicle‐related traits are important agronomic traits which directly associated with grain yield. In this study, we investigated quantitative trait loci (QTLs) associated with panicle‐related traits using a set of 265 introgression lines (ILs) of common wild rice (Oryza rufipogon Griff.) in the background of Indica high‐yielding cultivar Guichao 2 (O. sativa L.). A total of 39 QTLs associated with panicle‐related traits including panicle length (PL), primary branch number (PBN), secondary branch number (SBN), spikelet number per panicle (SPP) and spikelet density (SD), were detected in the ILs with single‐point analysis. The alleles of 20 QTLs derived from wild rice showed positive effects, and some QTLs, such as, QPl1b for PL, QPbn8 for PBN, QSd4 and QSd11b for SD and QSpp4 for SPP showed larger positive effects, providing good candidates and useful information for marker‐aided improvement of yield potential of rice. Most of the QTLs controlling SPP, SBN and SD were located in cluster or closely linked on chromosomes, and the directions of their additive effects were consistent, which explained the genetic basis of significant correlations between their phenotypic characters.     

Mapping and validation of QTLs for rice sheath blight resistance

Sheath blight, caused by Rhizoctonia solani, is one of the most serious diseases of rice. Among 33 rice accessions, mainly from National Institute of Agrobiological Sciences (NIAS) Core Collection, we found three landraces from the Himalayas—Jarjan, Nepal 555 and Nepal 8—with resistance to sheath blight in 3 years’ field testing. Backcrossed inbred lines (BILs) derived from a cross between Jarjan and the leading Japanese cultivar Koshihikari were used in QTL analyses. Since later-heading lines show fewer lesions, we used only earlier-heading BILs to avoid association with heading date. We detected eight QTLs; the Jarjan allele of three of these increased resistance. Only one QTL, on chromosome 9 (between markers Nag08KK18184 and Nag08KK18871), was detected in all 3 years. Chromosome segment substitution lines (CSSLs) carrying it showed resistance in field tests. Thirty F₂ lines derived from a cross between Koshihikari and one CSSL supported the QTL.     

水稻(Oryza sativa)感光抑制基因Hybrid Rice Photoreceptor Suppressor Gene 1(HRPSG1)的定位与分析

为了发掘更多的水稻抽穗期调控基因,完善相关基因调控网络,本课题组在水稻品系‘神9A’中发现一个能够抑制感光的基因,暂命名为Hybrid Rice Photoreceptor Suppressor Gene 1(HRPSG1)。遗传分析表明该性状受一对隐性核基因调控。通过杂交不育系配组方法与分子标记技术将该基因定位于第10条染色体长臂中段SSR-15和SSR-21之间,遗传距离分别为0.022 cM和0.025 cM,物理距离为115 kb。通过测序发现LOC_Os10g32600的外显子有两处碱基的突变,因此初步认为LOC_Os10g32600就是‘神9A’中抑制感光的基因。荧光定量PCR结果显示,水稻抽穗期相关基因DTH8和HD1在‘神9A’中的表达量急剧下降,分别仅有‘Q6A’的0.34和0.26。该结果为下一步HRPSG1基因的功能分析提供了帮助。     

Genetic regulation of growth and nutrient content under phosphorus deficiency in the wild barley introgression library S42IL

Phosphorus (P) is an important macronutrient required for plant growth and yield formation. Since decades, breeders aim to optimize P efficiency in crops. We studied a set of 47 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) in hydroponic culture to identify quantitative trait loci (QTLs) improving growth and nutrient content under P deficiency. Applying a mixed model analysis, a total of 91 independent QTLs were located among 39 ILs, of which 64 QTLs displayed trait‐improving Hsp effects. For example, an unknown Hsp allele on barley chromosome 4H increased shoot dry weight under P deficiency in three overlapping ILs by 25.9%. Likewise, an Hsp allele on barley chromosome 6H increased root dry weight under P deficiency in two overlapping ILs by 27.6%. In total, 31 QTLs confirmed Hsp effects already identified in previous field and glasshouse experiments with the same ILs. We conclude that wild barley contains numerous trait‐improving QTL alleles, which are active under P deficiency. In future, the underlying genes can be subjected to cloning and, simultaneously, used in elite barley breeding.     

A QTL for early heading in wheat cultivar Suwon 92

Heading date is an important trait that determines wheat adaptation to environments. A recombinant inbred line (RIL) population derived from CI 13227 × Suwon 92 was employed to tag the quantitative trait locus (QTL) for early heading in Suwon 92. This population was phenotyped for heading date in 1994, 1995, and 1997, and analyzed with AFLP and SSR markers. Two AFLP markers (XGCTG.CGCT118 and XGCTG.CGCT60) closely associated with heading date were identified. Across years, XGCTG.CGCT118 and XGCTG.CGCT60 explained 40.4% and 32.2% of the total phenotypic variances, respectively. Interval analysis revealed a major QTL for heading date, designated QHd.pser-2DS, between AFLP marker XGCTG.CGCT118 and SSR marker Xgwm261. Based on the linkage map, QHd.pser-2DS was about 41.2 cM proximal to the distal end of chromosome 2DS, and explained 40.5% of the phenotypic variance across three years. The identified markers associated with the early heading QTL have the potential to be used in wheat breeding programs.     

QTL analysis for alkaline tolerance of rice and verification of a major QTL

Alkaline stress causes injuries to rice seedlings in many parts of the world and is therefore an important factor affecting rice production in such areas. In this study, we preliminarily located quantitative trait loci (QTLs) for survival days of seedlings (SDS) and the concentrations of Na⁺ and K⁺ in shoots (SNC and SKC) and roots (RNC and RKC) under alkaline stress using an F_2:3 population, which was derived from a cross between Caidao and WD20342 with 151 simple sequence repeat (SSR) markers. A total of seven QTLs were detected. Of these QTLs, qSNC3 had the largest effect, which explained 21.24% of the total phenotypic and is a major QTL. Next, a mapping population consisting of 190 BC₂F₂ plants was constructed using WD20342 as a donor parent to verify qSNC3. As a result, qSNC3 was delimited to an 81.7‐kb region between markers RM1221 and RM4404. In this region, LOC_Os03 g62500 and LOC_Os03 g62620 exhibited different expression between Caidao and WD20342 under alkaline stress. These results provide a basis for identifying genes related to alkaline tolerance in rice.     

一个具有主效晚抽穗基因的水稻染色体片段代换系的鉴定、形态分析及Ehd4-2定位

抽穗期是决定水稻品种种植地区和季节适应性的重要农艺性状,鉴定抽穗期基因对水稻生产具有重要意义。本研究采用高代回交和SSR标记辅助选择相结合的方法获得了1个以日本晴为受体亲本、西恢18为供体亲本的含有1个控制晚抽穗表型的主效单基因的水稻染色体片段代换系Z315。Z315携带来自西恢18的5个代换片段,分布于第1、第3、第6和第7染色体上,平均代换片段长度为7.39 Mb。Z315的叶绿素含量、株高、穗长、倒一节间长、倒二叶长、倒三叶长、有效穗数、每穗实粒数和总粒数均显著高于受体日本晴,暗示其代换片段可能携带这些性状的QTL。进一步利用日本晴与Z315杂交产生的F1和F2群体对晚抽穗基因进行遗传分析和分子定位。该晚抽穗表型受1对隐性核基因控制,最终将该基因定位于第3染色体RM14283和RM6349之间,物理距离为233 kb。对该区间进行候选基因预测和测序,发现1个与抽穗相关的编码锌指蛋白的基因LOC_Os03g02160在日本晴和Z315间存在差异,该基因可能与Ehd4等位,称作Ehd4-2。由于染色体片段代换系除代换片段外与受体亲本一致,因此本研究无论对进一步分离其他QTL还是进行基因聚合育种均具有较大利用价值。     

Photoperiod sensitivity gene controlling heading date in rice cultivars in the northernmost region of Japan

Rice is grown in diverse environments at latitudes ranging from 53^°N to 40^°S. In Japan, Hokkaido is the northernmost rice cultivation region(42–45^°N latitude). Only extremely early maturing (heading) varieties that have extremely low photoperiod sensitivity are adapted to this area. Heading date is the most important trait in adaptation to this particular environment. Also, the efficient manipulation of heading date is a crucial component of rice improvement. To determine the genetic basis for heading date among cultivars grown in Hokkaido, the heading behaviour was analyzed. Clear segregations were observed. To estimate the photoperiod sensitivity of the genes involved, the cultivars and F₁ plants from crosses between the cultivars were grown under different daylength conditions. The results indicated that the genes controlling heading date are photoperiod sensitive, suggesting they play important roles in the northernmost rice cultivation regions in Japan, to which only cultivars with extremely low photoperiod sensitivity are adapted. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetics and identification of molecular markers linked to resistance to loose smut (<Emphasis Type="Italic">Ustilago tritici</Emphasis>) race T33 in durum wheat

This study was conducted to determine the genetic control of resistance to loose smut caused by Ustilago tritici race T33 in two durum recombinant inbred line populations (DT662 × D93213 and Sceptre × P9162-BJ08*B) and to identify molecular markers linked to the resistance. Resistance in both populations was controlled by single genes. Two SSR markers were linked with loose smut resistance in the Sceptre × P9162-BJ08*B population. In DT662 × D93213, two AFLP, two wheat SSRs and one SCAR markers were linked to resistance. The SCAR marker, 3.2 cM distal to the smut resistance locus (Utd1) on chromosome 5BS, accounted for up to 64% of the variability in disease reaction; the other markers were proximal to Utd1 at genetic distances ranging from 5.9 to 35.9 cM. SSR markers Xgwm234 and Xgwm443 segregated in both crosses suggesting a common resistance gene. The SCAR and SSR markers can be used effectively for marker assisted selection to incorporate loose smut resistance into durum cultivars.     

Development of high yielding IR64 × <Emphasis Type="Italic">Oryza rufipogon</Emphasis> (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC₂F₆ progenies, selected from among more than 100 BC₂F₅ progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.     

水稻黄绿叶突变体ygl209的遗传分析与目标基因精细定位

水稻叶色突变体是研究高等植物光合作用、叶绿体发育和叶绿素代谢的重要材料。从水稻转基因育种材料中国91与镇稻88的BC4F3后代中分离到稳定遗传的粳型黄绿叶突变体ygl209,与野生型亲本镇稻88相比,突变体ygl209在苗期、分蘖期及抽穗期叶片中叶绿素a、叶绿素b和类胡萝卜素含量均显著降低,其中叶绿素b降幅最大;其他农艺性状中抽穗期、株高、有效穗数、主茎穗总粒数、结实率和千粒重无显著变化。遗传分析表明,ygl209的黄绿叶突变性状由1对核隐性基因控制。应用(ygl209/9311)F2、F3分离群体,将ygl209的叶色突变基因定位于第1染色体着丝粒附近571.6 kb的染色体区段内。对区段内与叶绿体发育有关的基因LOC_Os01g31110序列测定,ygl209突变体中LOC_Os01g31110基因的编码区1390位(位于第5外显子)上碱基由C转换成G,使编码蛋白序列由丙氨酸(Ala)变成了甘氨酸(Gly),推测LOC_Os01g31110即为ygl209的候选基因。     

栽培稻与普通野稻杂交杂种优势和农艺性状的遗传分析

按不完全双列杂交方式组配了12个栽培稻与普通野稻种间杂交组合,定量分析其杂种优势和利用加性-显性模型对11项农艺性状进行遗传分析。结果表明：12个栽野交组合的平均杂种优势为-0.608~3.031,穗数和籽粒长宽比表现强优势是其主要特征。栽野交的穗数、籽粒长宽比、结实率和抽穗期的优势显著高于籼粳交。各性状具有较高的广义遗传力(0.50~0.92);狭义遗传力为0.24~0.84,籽粒长宽比和抽穗期的狭义遗传力较高,其它性状中等偏低。各项农艺性状间具有显著或极显著水平的表型相关和遗传相关,可作为育种间接选择时的有效参考指标。     

高温对一季晚稻结实率与产量的影响及其防御技术

为了寻找湖南省主推一季晚稻品种最佳播种期,避开水稻幼穗分化的减数分裂期与抽穗期的高温热害,通过分期播种,研究不同时期的气温对一季晚稻品种幼穗分化的减数分裂、抽穗灌浆结实及产量的影响,同时调查了湖南省大面积生产的高温热害。研究与调查结果表明：在湘中地区,生育期相对较长的一季晚稻品种最佳播种期是5月20日左右,生育期相对较短的一季晚稻品种最佳播种期是5月30日左右,最安全的幼穗分化的减数分裂期是8月13日后,最安全的抽穗灌浆期则是8月下旬。     

Mapping and candidate gene analysis for a new top spikelet abortion mutant in rice

Grain numbers is one of the determinations for rice yield and directly associated with spikelet numbers per panicle and its normal development. Lots of genes responsible for spikelet numbers and spikelet early development have been identified, but the molecular information about the spikelet development at later development is still limited. Here, we isolated a rice spikelet abnormal development mutant, which shows degenerated spikelet at the top panicle and named aborted top spikelet mutant 1(Ats1). The spikelets derived from the middle and bottom branches per panicle of Ats1 show normal development with those of wild type. However, a large number of branches and spikelets with arrested development were often observed only on apex panicle. The abnormality did not appear until the stage In8 when rachises elongate rapidly and reproductive organs get mature, based on observations through SEM analysis. The aborted spikelet could develop the complete floral organs with a pair of rudimentary glume, a pair of empty glume, two lodicule, six stamens and one carpel. But all these floral organs did not develop maturity. Genetic analysis on two F₂ populations indicated that the Ats1 was controlled by a single dominant gene. By using bulked segregant analysis of F₂ population developed from Ats1 crossing with Songjing6, ATS1 was mapped on chromosome 8 between RM3819 and RM5556. Then, the fine mapping was performed with 1078 F₂ population developed from Ats1 and IR36. The ATS1 locus was finely mapped in an 85.7 kb region between RM22448 and STS8‐2 with 8 genes according to the rice annotation project database. Sequence analysis of the candidate genes within the delimited region of the Ats1 and Akihikari showed two‐nucleotide changes, including single‐nucleotide substitutions corresponding to an amino acid substitution from asparagine to lysine acid in exons 3 and a 1‐bp deletion resulting in a premature stop codon in exon 22 at the candidate gene, LOC_Os08g06480. A cleaved amplified polymorphic sequence (CAPS) marker, CAPS‐ats1, was developed from the 1‐bp deletion site. The complete cosegregation of the CAPS genotypes with the matching phenotypes were observed in the F₂ populations. This suggested that Os08g06480 is most likely the ATS1 gene. These results will provide more information for better understanding of the molecular mechanism governing top spikelet abortion within a short developmental period.     

多年生长雄蕊野生稻感光性的遗传分析

非洲的长雄蕊野生稻(Oryza longistaminata)具有多年生、抗病、抗虫、耐寒、耐旱等优良特性,可用于栽培稻的遗传改良。但其感光性强,长日照下不抽穗。为了在分子标记辅助育种过程中排除不需要的强感光性,须先找到长雄蕊野生稻中控制感光性的QTL。感光性是指水稻受日照长短的影响而改变其抽穗期的特性。抽穗期作为水稻重要的农艺性状,与产量有着密切的联系。本研究以长雄蕊野生稻(Oryza longistaminata)为父本,栽培稻巴利拉(Balilla)为母本杂交构建的F2群体为研究材料。对F2群体的抽穗期性状进行QTL定位分析,共得到6个控制水稻抽穗期的QTL,这些QTL分别位于第2号、第4号、第8号和第9号染色体上。在两年长日照下的F2群体中都检测到第8号染色体上的qDTH-8-1位点,但短日照下未检测到该位点,说明其跟感光性相关。qDTH-8-1是一个主效位点,对抽穗期表型贡献率最大,其中包含已被克隆的DTH8/GHD8基因。此外,我们还检测到另外4个已被定位但未被克隆的位点qDTH-4-1、qDTH-8-2、qDTH-9-1和q DTH-9-2,他们在本群体中的效应不大。结果表明,长雄蕊野生稻的感光性主要由qDTH-8-1控制,育种后代中要注意检测该位点的基因型。通过检测长雄蕊野生稻中的抽穗期QTL并进一步克隆到基因,这有助于深入了解野生稻强感光性的遗传机理,为水稻品种改良提供基因资源。     

云南3种野生稻中抗白叶枯病基因的鉴定

白叶枯病是水稻生产上最重要的细菌性病害之一,培育抗病新品种是防治白叶枯病最经济有效的途径。然而,栽培稻来源的抗病基因数量有限,并且部分抗病基因的抗病谱窄。因此,从野生稻中发掘抗病基因,将有利于培育抗病谱广且抗病能力强的水稻新品种。本研究通过抗性鉴定和PCR分析,检测云南野生稻中的抗白叶枯病基因。结果表明,云南野生稻对2个代表性白叶枯病菌Y8和PXO99具有不同程度的抗性,疣粒野生稻甚至达到免疫的程度。功能标记检测结果显示,3种野生稻中均不含xa5、xa13和Xa21抗病基因,元江普通野生稻含Xa23和Xa3/Xa26基因或其同源基因,景洪普通野生稻中含Xa1、Xa3/Xa26和Xa27基因或同源基因,药用野生稻含Xa3/Xa26基因或同源基因,而疣粒野生稻含有Xa27抗性基因。本研究结果为进一步发掘和克隆云南野生稻中的抗白叶枯病新基因提供了理论参考。