摘要
水稻是世界上最主要的粮食作物。长期以来,由于人口增长和环境问题及随之而来的粮食安全问题,提高水稻产量一直是我国水稻育种和生产的重中之重。但是近年来,随着生活水平的提高,人们对稻米品质提出了更高的要求。同时,国际粮食市场的竞争十分激烈,也促使了我国水稻育种目标从片面的高产转向高产与优质并举。因此品质的遗传学研究成为水稻研究中重要的一部分。本文从两种角度研究了稻米的品质性状：1)从籼粳品种间寻找主效的优质等位变异,改良稻米品质；2)从突变体角度寻找和研究调控稻米品质形成网络中的必要元件。
稻米虽然仅含2-3%的脂质,但具有独特的营养功效,并能影响其他的营养品质。前人研究表明稻米脂肪含量受多基因控制。稻米脂肪的研究仅限于经典遗传学分析和单环境QTL检测,其遗传研究有限。本研究利用两套来源于不同亲本的定位群体,对稻米脂肪性状进行QTL稳定性分析。同时,以高脂肪的巨大胚品种w025为材料图位克隆了巨大胚基因(OsGE)。此外,本研究还初步定位了一个相关稻米粒形的基因(SGL)。具体内容如下：
1.稻米脂肪积累相关QTL检测及环境稳定性分析
利用Sasanishiki/Habataki//Sasanishiki回交重组自交系群体对稻米脂肪积累相关的两个性状(脂肪含量和脂肪指数)进行单环境QTL分析。在稻米脂肪含量方面,共检测到5个QTL。在脂肪指数方面,共检测到3个QTL。同时,利用以Sasanishiki为背景Habataki为供体的CSSL群体,对上述QTL进行验证和环境稳定性分析。结果显示稻米脂肪含量的QTL和稻米脂肪指数的QTL(除qFl2外)都能被CSSL证实并且在环境中是稳定表达。本研究还发现第3染色体的R2778-C1452标记区间和第11染色体的C1172-G1465区间存在稻米脂肪含量和稻米脂肪指数QTL共位点现象。本研究将有助于理解水稻脂肪积累的遗传基础,同时为分子标记辅助选择改良稻米脂肪提供一定的理论指导。
2.稻米脂肪含量QTL的稳定性分析及相关生理生化分析
利用以Koshihikari和Kasalath为亲本衍生而来的BIL群体和CSSL群体,对稻米脂肪含量QTL进行了三个环境的稳定性分析。结果显示定位于第7染色体的两个主效QTL (qFC7.1和qFC7.2)在两套群体三个环境中都能稳定表达。而后选择了4个来源于相同亲本组合CSSL家系,其中三个家系(SL219、SL220和SL 221)聚合了两个QTL, SL222家系仅携带Kasalath qFC7.2等位基因。6个环境的表型检测显示,这4个CSSL家系的稻米脂肪含量都显著高于背景亲本。其中的3个家系由于两个QTL的聚合而使其脂肪含量显著高于仅携带单QTL的SL222,验证了qFC7.1的效应及两个基因聚合的效应。同时,对这4个家系的生理生化分析显示：这两个QTL均能大幅度提高米胚油含量,仅携带Kasalath qFC7.2等位基因的SL222家系的蛋白含量和直链淀粉含量相比于背景亲本没有显著变化。萌发实验也显示4个CSSL家系萌发速度较背景亲本快,从另一侧面说明这两个QTL提高了稻米储藏性脂肪的积累。本研究还利用分子标记筛选SL220/Koshihikari的回交次级F2群体,找到了3个家系仅携带qFC7.1,并且这3个家系较背景亲本脂肪含量都极显著提高,直接证明qFC7.1的加性效应。此外,在qFC7.2标记区间内找到了一个相关脂肪合成的酶(3-氧酰基-酰基载体蛋白)基因,测序结果显示：双亲在cDNA上存在多个单碱基差异。这些证据有助于进一步了解稻米脂肪含量的遗传和分子基础,并为改良稻米脂肪提供了理论基础。
3.高营养高脂肪含量的巨大胚突变体基因OsGE的图位克隆
米胚的大小直接影响到稻米籽粒的脂肪含量。本研究的材料是本实验室的大胚品种w025。米胚石蜡切片分析结果显示：w025的大胚表型主要是由盾片的伸长所造成。而后利用其与9311衍生的F2群体对大胚基因OsGE进行图位克隆,并将OsGE基因初步定位在第7染色体RM21930和RM234之间约950kb的区域。而后用进一步扩大群体将OsGE基因精细定位在RM21930和InDelE之间95Kb的区域,并与标记IndelG共分离,包含两个BAC克隆。NCBI在该区间收录了一个与米胚大小发育相关基因,编码一个细胞色素P450蛋白。扩增、测序和比对显示在该基因区间内存在一个单碱基变化导致w025翻译提前终止,从而导致该基因失活。本研究为后续的基因功能分析提供遗传基础。
4.短粒基因SGL的初定位
粒形影响着外观品质和产量。本研究利用了一个多向表型的短粒突变体(short grain length,sgl)对其基因进行了初步定位。表型研究显示sgl在粒形、穗形、株高和节间长度上与野生型Kitaaki具有显著差异。sgl突变体是转基因过程中突变的植株。TAIL-PCR侧翼序列分析发现外源片段插入了一个位于第一染色体的多聚蛋白编码基因。而后利用sgl突变体与冈46B衍生的F2群体(7000株)对SGL基因进行初步定位。但是由于籼-粳交背景的干扰,F2群体粒形分离比严重偏离,仅选到40株短粒极端个体。利用BSA法在第五染色体上筛选到与粒形具有较好连锁关系的标记G5-9。而后利用F2群体将SGL基因初步定位于G5-9-1510之间127Kb的区间内。该定位的区间内有17个ORF框,其中包括泛素连接酶基因和多种调控基因。这些基因都可能与稻米颖壳和籽粒发育具有密切的关系。本实验为进一步精细定位及分子功能研究提供遗传基础。
Rice is a main cereal food for the population of world and China. Because of the increase of population and food security problem, improving the yield is the most important goals of rice breeding programs in our coutry. However, with the improvement of people's life quality and the fierce global rice market competition, rice quality improvement has become one of the most important goals in rice breeding programs. Here, two different methods were used:1) QTL analysis was used to search useful natural allele for rice quality.2) mapping cloning of genes underlying mutant for rice quality was used to find the essential elements controling rice quality.
Though the fat or oil in rice grain is low (i.e.,2-3%) and concentrated in germ and bran fraction, its unique healthy benefits has been drawing people's attention. At the same time, it is a key determinant of the processing and cooking quality of rice. So far, the genetic studies on fat had been carried out mainly by classical quantitative genetic methods and single-environment QTL detection. Thus, the genetic information on the environmental stability of QTL, gene action of QTL in the new genetic background, and DNA markers closely linked to target QTL are particularly lacking. To better elucidate genetic basis of rice fat accumulation, Four different populations were used to analysis environmental stablity across different environments. At the same time, we identified the OsGE gene, which can enhance rice fat accumulation by increasing rice embryo size. Besides, we also identified a short grain length mutant (SGL), and the SGL gene were mapped on chromosome 5. The main results are as follows:
1. Identification of stably expressed QTL for grain fat accumulation
A total of 85 inbred lines derived from the backcross between Sasanishiki (japonica, as the recurrent parent) and Habataki (indica) were used to detect QTL for rice fat acumulation including fat content, brown rice weight and fat index. Five QTL for fat content, three QTL for brown rice weigth and three QTL for fat index were mapped on chromosome 1,3,6,7,10,11 and 12, explained 5.84-28.46% of the phenotypic variance. Then all the QTL for fat content and fat index were further confirmed across two different environments by some chromosome segment substitution lines (CSSLs), where Habataki was used as the donor parent and Sasanishiki as the recurrent parent, except qFI2. Some QTL affecting fat content and fat index were mapped on the same genome regions. Co-localization of these QTL can provide an explanation for the genetic basis of correlation between fat content and fat index.
2. Identification of two loci increasing grain fat content in rice and physiological analysis of their function (Oryza sativa)
The BIL population and CSSL population derived from Koshihikari and Kasalath were used to analysis stable-expressed QTL across three environments. Two stable QTL (denoted as qFC7.1 and qFC7.2) for fat content with large effect were mapped on chromosome 7 in two population across three environments. Four CSSLs were selected to further analysis. Six-environment data on fat content of the four CSSLs confirmed the effect of qFC7.1 and qFC7.2 with high repeatability. Further analysis of these CSSLs on physiology and biochemistry showed that qFC7.1 and qFC7.2 can enhance rice storage fat and embryo fat without other adverse effects. To obtain a CSS line only harboring qFC7.1, we developed a SBC3F2 population (n=2000) from Koshihikari and SL220 pryminding qFC7.1 and qFC7.2. we selected three SBC3F2 lines only habording qFC7.1 by MAS. T-test derectly confirmed the present of qFC7.1. In our marker interval of qFC7.2, we found there was a candidate gene encoding 3-oxoacyl-[acyl-carrier-protein], which played a role on fat synthesis. cDNA sequence blast showed that there was some single nucleic acid difference between Koshihikari and Kasalath. All these results can help us for further study on genetic basis of rice fat.
3. Mapping cloning of OsGE gene which can can enhance rice fat accumulation by increasing rice embryo size.
Embryo size-related genes can be used for enchancing rice grain nutrition, especially rice fat. w025 is a new variety derived from chemical inducement and cross breeding method. It is characteristic for its giant embryo. To investigate the effects of embryo size, we conducted microscopy analysis. The result showed that w025has an enlarged scutellum. To map the ge locus, we generated F2 mapping population derived from a cross of the w025 and the cultivar 9311. We mapped the ge to an interval between RM21930 and RM234 on Chromosome 7. To narrow down the search for a candidate gene affected in ge, a larger F2 mapping population consisting of more than 10000 plants, of which 1000 segregants showing the ge mutant phenotype were used for fine-mapping. Between markers RM516 and RM164, we further developed one SSR marker and two InDel markers. The ge locus was finally located in a 95-kb DNA region between SSR marker RM21930 and InDel marker InDelE. In this interval, a gene related with embryo size was collected by NCBI. To define the molecular lesions of ge mutant, the ORF from from wild type and w025 were amplified by RT PCR and were sequenced. Comparison of the sequences revealed that the ORF carries a single nucleotide mutation, which cause premature termination, resulting in a truncated polypeptide.
4. primary mapping of SGL gene
In our study, we also isolated a short grain length mutant (SGL). Comparing with wildtype Kitaaki, SGL has distinguished phenotype on grain size, panicle characters, heading date and plant height. Since SGL was derived from transgene lines, the TAIL-PCR was used to analysis the gene which was knocked out by exogenous DNA. The result showed that the knock-out gene is mapped on chromosome 1and encode a polyprotein. To map the SGL locus, we generated F2 mapping population derived from a cross of the SGL and the cultivar G46B. Then We mapped the SGL to an interval between G5-9 and 1510 on Chromosome 5, a 127-kb DNA region. These results are useful in map-based cloning of GSL gene.
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