新疆小麦（Triticum petropavlovskyi Udacz.et Migusch.，2n=6x=42，AABBDD）是我国新疆特有的六倍体栽培裸粒小麦。新疆小麦与普通小麦在形态学方面有许多明显的区别，如长穗、长颖、长粒和高千粒重等，特别是长颖表型，是新疆小麦最突出的性状。目前，国内外学者对新疆小麦的起源演化过程和长颖性状的遗传分析进行了许多研究，但仍然未有定论，也尚未克隆到控制新疆小麦长颖的基因P1。颖壳长度是重要的农艺性状，颖壳不但能作为源器官进行光合作用产生同化物，也能作为库器官贮存营养物质。较长的颖壳对增加粒长、粒重有着重要的作用。因此对控制新疆小麦长颖的基因进行精细定位、克隆和功能验证，不仅可以拓宽栽培小麦遗传基础，而且为进一步利用长颖性状提高小麦产量提供参考，也可为新疆小麦的起源进化提供证据。 实验室前期以新疆小麦品系“洛浦”为母本，普通栽培小麦品种扬麦158为父本，构建了一个包含191个BC2F10家系染色体片段置换系(Chromosome Segment Substitution Line，CSSL）群体。使用小麦55K芯片对CSSL群体的家系进行SNP分型，结合表型数据，检测到7A染色体短臂127.5Mb-133.2Mb区域有一个控制颖长的QTL，并且与产量性状（千粒重）显著相关；以其中一个长颖的近等基因系2017CY92与扬麦158杂交构建的次级分离群体，通过筛选交换单株，将控制颖长的QTL进一步定位于7AS的128.8-130.3Mb。本研究在前期研究的基础上，利用CSSL群体中的另一个长颖的近等基因系LZP87与扬麦158构建F2次级分离群体，通过交换单株筛选和定位区间内分子标记加密，对新疆小麦控制长颖的基因进行了精细定位，结合转录组分析和目标区域基因序列差异分析，克隆了控制长颖的P1基因，该基因编码SVP类型的MADS-box转录因子，被命名为TaVRT-A2（TaVRT2），通过创制突变体、转基因功能互补验证等方法，证明了TaVRT2基因是控制新疆小麦长颖的P1基因。取得的主要研究结果如下： 1. 利用次级分离群体对新疆小麦长颖基因进行精细定位 在前期定位的区间内（7AS，127.5Mb-133.2Mb），根据中国春参考基因组序列，设计了56对SSR引物。利用这56对SSR引物分别在LZP87和扬麦158之间进行新疆小麦长颖基因TaVRT2的精细定位、克隆与功能验证 II 扩增，共筛选到16个双亲之间有多态扩增的SSR分子标记。选取其中扩增条带清晰的9个SSR分子标记在522个F2群体中扩增，筛选了22株交换单株，结合表型鉴定结果，最终将定位区间缩小到物理位置128.8-129.6Mb，约897Kb。该定位区间内共有12个已经注释的基因。 2. 利用转录组数据确定候选基因 为了确定定位区间内候选基因，本研究分别对长颖渐渗系家系LZP87和扬麦158的5个穗发育时期（护颖原基分化期、外颖分化期、花药原基发育时期、四分体时期和抽穗期）的穗子取样进行了转录组测序。结果显示在定位区间的12个基因里，一个SVP类型的MADS-box基因TaSVP-A2（TaVRT-A2）在长颖材料的5个时期均有较高的表达水平，而在正常颖扬麦158中几乎检测不到表达；其他11个基因或检测不到表达（6个），或可检测表达，但表达量在两个材料中没有明显差异（5个），选取5个可检测表达但无差异的基因进行序列克隆后比较，也未发现差异。因此，初步确定TaVRT2为新疆小麦长颖基因P1的候选基因。 3. TaVRT2的克隆与序列分析 对TaVRT2的克隆结果显示：新疆小麦洛浦和中国春（与扬麦158）仅在第一内含子中有一段插入-缺失（Indel）差异，其余部分的基因组DNA序列均完全相同。中国春和扬麦158第一内含子中有一段560bp的序列，对应新疆小麦洛浦是一段157bp的序列。根据此差异开发了Indel标记，可以区分560bp和157bp序列差异，利用该标记对191个CSSL家系进行了基因分型，结果发现凡是157bp类型的单株均表现为长颖，而560bp类型的单株均表现为正常颖。表明该标记与颖长性状是共分离的，进一步证明TaVRT-A2是控制新疆小麦长颖P1基因。 4. 新疆小麦洛浦短颖突变体的创制以及利用突变体验证候选基因 用EMS诱变新疆小麦洛浦的种子，在M2代发现了一个颖壳明显变短的突变体，M3代发现其短颖性状可以稳定遗传，在验证其新疆小麦背景后，分别克隆了TaVRT-A2基因的gDNA和cDNA序列，发现其gDNA的第六内含子5’端起始的GA剪切位点，第一个碱基G突变成了A，克隆cDNA发现，第六内含子包含在cDNA序列中，表明该突变导致成熟的mRNA中第六内含子不能被剪切，从而使得突变体编码的氨基酸发生了移码突变，导致基因编码提前终止，蛋白序列变短，我们推测正是由于突变体编码的氨基酸序列变短使其失去了调节颖壳变长的功能。通过突变体分析，进一步证实了控制新疆小麦长颖的P1基因就是TaVRT-A2。 5. TaVRT-A2基因的亚细胞定位和利用转基因验证TaVRT2基因的功能 利用农杆菌注射烟草进行瞬时表达，对TaVRT-A2基因进行了亚细胞定位分析，摘要 III  结果发现该基因定位于细胞核，符合其转录因子的特征。为验证TaVRT-A2基因的功能，利用农杆菌介导的转基因技术，在小麦品种Fielder中转化TaVRT2基因，使用玉米泛素基因启动子驱动其组成型表达。结果显示，在转TaVRT-A2的各个植株中，其颖壳长度相对于Fielder受体均有明显的伸长，而且转TaVRT-A2基因相对表达量越高，颖壳伸长越明显，表明TaVRT-A2具有明显的剂量效应。转基因功能互补实验进一步证明控制新疆小麦洛浦长颖的P1基因为TaVRT-A2。 6. 新疆小麦起源于波兰小麦 本研究发现了新疆小麦与普通小麦在TaVRT-A2第一内含子的两种不同单倍型，在两份波兰小麦中进行克隆，发现波兰小麦也属于157bp类型；基于此差异开发的Indel标记，对小麦属的多个典型的长颖或正常颖品种进行了基因分型，发现了新疆小麦与17份世界各地引种的波兰小麦均同属于157bp类型。表明六倍体新疆小麦由新疆当地或其他地区引进的六倍体小麦与四倍体小麦波兰小麦杂交后代中选育而来，P1基因克隆为新疆小麦起源于波兰小麦这一观点提供了强有力的证据。

The Chinese wheat landrace Xinjiang Rice Wheat (Triticum petropavlovskyi Udacz. et Migusch., 2n=42), known as ‘Daosuimai’ or ‘rice-head wheat’ was discovered in the western Tarim basin in Xinjiang Uygur Autonomous Region, China. T. petropavlovskyi featured by the morphology with long glume and long oval-shaped grain. Interestingly, it also has higher grain weight, long spike length and high protein content. At present, many studies focused on the origin and evolution process of Triticum petropavlovskyi and genetic analysis of long glume traits, but there is still no obvious conclusion, and the long glume gene has not been cloned. The length of the glume is an important agronomic trait. The glume can not only be used as a source organ for photosynthesis to produce assimilation, but also can be used as a sink organ to store nutrients. Longer glumes play an important role in increasing grain length and grain weight. Therefore, the fine mapping, cloning and functional verification of the long glume genes that control Triticum petropavlovskyi can not only broaden the genetic basis of cultivated wheat, but also provide a reference for further use of long glume traits to increase wheat yield, and also for better understanding the evolutionary history of Triticum petropavlovskyi. In the early stage of our laboratory, a CSSL (Chromosome Segment Substitution Line, CSSL) population containing 191 lines was constructed coming from Triticum petropavlovskyi Luopu and the common cultivated wheat variety Yangmai 158.The LP/YM CSSL population was genotyped by Wheat55K Array. Association analysis of 138 SNP markers on 7A and GL phenotype data of the CSSLs showed that P1pet could be located within two SNP markers AX-109335244 and AX-108807463, corresponding to a genome region from 127.91 to 133.22 Mb on 7AS. Based on the previous research, this study used the F2 secondary segregation population coming from LZP87 and Yangmai 158. By developing more molecular markers and the phenotype of F2 individual plants in the positioning interval, the genes that control long glumes in wheat have been finely mapped. 新疆小麦长颖基因TaVRT2的精细定位、克隆与功能验证 IV Combining transcriptome analysis, gene cloning, mutant creation, genetic modification and other methods, it proved that the TaVRT2 gene regulated the glume elongation of Triticum petropavlovskyi. The main research results obtained are as follows: 1. Using secondary segregating populations to fine-map the wheat glume gene in Triticum petropavlovskyi To further fine map the P1pet, 56 SSR markers were developed referring to the genome sequence of China Spring. The 56 SSR molecular markers were amplified in LZP87 and Yangmai 158 to screening the polymorphic markers. Sixteen molecular markers were screened and polymorphic between LZP87 and Yangmai 158. To fine map P1pet, a CSSL line LZP87 and YM were used to construct a secondary F2 mapping population. （LZP87×YM） F2 population was genotyped using nine molecular markers. Finally, P1pet gene was finely mapped between markers SNP41698 and SSR4, corresponding to a physical distance of 897 Kb from 128.8 to 129.6 Mb on 7AS. According to RefSeqv1.1 annotation of Chinese Spring genome reference, 12 genes were annotated and considered as candidates of the target gene. 2. Using RNA-seq data to identify candidate genes To predict the candidate for P1pet, gene expression profile of LZP87 and YM at five developmental stages was compared using RNA-seq). The seven of 12 candidate genes (G3- G9) were precluded because they barely expressed in most of the tested stages. The remained five gene were further analyzed based on their gene annotation, gene expression and sequence comparison. Gene G1, G10, G11 and G12 showed relatively high expression at all five stages, no obvious difference in expression level between LZP87 and YM was detected. Sequence comparison showed they are completely identical between LZP87 and YM. Gene G2 (TraesCS7A02G175200) encodes an SVP-like MADS-box transcription factor. Gene annotation showed G2 has two splice variants, TraesCS7A02G175200.1 (226aa) and TraesCS7A02G175200.2 (240aa). RNA-seq revealed significantly different gene expression patterns of G2 between LZP87 and YM at all tested stages, with a very high expression level in LZP87 while be barely expressed in YM. Therefore, we deemed TraesCS7A02G175200 as the candidate for P1pet. ABSTRACT V  3. Cloning and sequence analysis of TaVRT2 pet According to TraesCS7A02G175200.1, the 6113 bp genomic DNA sequences of P1pet, including 431 bp upstream of the start codon ATG to the termination codon TGA, was cloned from LP. The 6113 bp is corresponding to the 6516 bp sequences in the public Chinese Spring genome reference (designated as P1cs). Sequence comparison identified a sole polymorphism within their intron-1, showing by that a 560-bp sequence in P1cs was substituted by a 157-bp sequence in P1pet. To verify the association of this polymorphic locus with the elongated glume, a PCR-based molecular marker (SVPA2-indel) was developed. SVPA2-indel could simultaneously detect the presence of 560-bp deletion in P1cs and the 157-bp substitution in P1pet. SVPA2-indel was used to genotype 191 LP/YM CSSL lines All individuals with elongated glumes had the marker allele the same as LP, confirming TraesCS7A01G175200 is the candidate 4. The creation of Triticum petropavlovskyi Luopu short glume mutants and the use of mutants to verify candidate genes By EMS mutagenesis treatment of LP, a stable mutant line (designated as NAU32) with reduced GL was identified from the M2 population. The TaVRT2 pet was cloned from NAU32, and we observed a homozygous mutation in the guanine residue of the GT canonical splice acceptor site in intron-6, being a G>A transition at 4926-bp from the start codon of TaVRT2 pet. The cDNA from young spike of NAU32 was sequenced to determine the effect of the G4926A splice site mutation on TaVRT2 pet transcription. We did observe the change of fragment sizes in wildtype LP (681 bp) and mutant NAU32 (815 bp). Further sequencing of the cDNA clones showing that only mutant NAU32 had the sequence intron6, implying a failure of splicing due to the impairing in the mutated splice acceptor site. The non-splicing of intron-6 transcript in NAU32 results in a frame-shift and generates a premature termination codon at 15 bp in this intron. The truncation of the C-terminus 52 amino acids results in a shorter protein of only 174 amino acids (being 226 aa in wildtype). Compared with wildtype LP, NAU32 displayed reduced GL. This confirmed P1pet’s candidate is TaVRT2 pet, which is critical for elongated glume in wildtype T. petropavlovskyi. We assumed the truncated protein in mutant lost the function in regulating glume elongation. 新疆小麦长颖基因TaVRT2的精细定位、克隆与功能验证 VI 5. Subcellular localization of TaVRT2 pet gene and verification of the function of TaVRT2 pet gene by transgene Using the transient expression system mediated by Agrobacterium in the tobacco system, the TaVRT2 pet gene was analyzed for subcellular localization, and it was found that the gene was localized in the nucleus. In order to verify the function of the TaVRT2 pet gene, Agrobacterium-mediated transgenic technology was used to overexpress the TaVRT2 pet gene in the wheat variety Fielder. The results showed that the length of the glume of transgenic plant with overexpression of TaVRT2 pet was significantly longer to the receptors, and also found that transgenic plant with the higher relative expression has the more elongation of the glumes, and the texture and color of the glumes were closer to that of Triticum petropavlovskyi Luopu. This result fully demonstrated that the gene controlling Triticum petropavlovskyi Luopu glume length is TaVRT2 pet. 6. Triticum petropavlovskyi originated from Triticum polonicum Two different Indel types in the first intron of TaVRT2 pet in Triticum petropavlovskyi and common wheat were detected in Triticum petropavlovskyi and common wheat. the Indel marker was developed based on this difference, and genes for many typical long glume or normal glume varieties of the Triticum genus were carried out. Marker analysis of 278 wheat varieties using SVPA2-indel indicated they were all P1cs allele, indicating the “157-bp sequence” in intron-1 was only present in T. petropavlovskyi. The P1pol was cloned from T. polonicum (Accession No. CItr 3282), and the genome sequence was 100% identical to P1pet. Thirteen T. polonicum lines including CItr 3282 were analyzed using the marker SVPA2-indel, and they all have 157-bp sequence in intron-1. It implied P1pet in T. petropavlovskyi may be introduced from tetraploid T. polonicum through the hybridization between T. polonicum and hexaploidy landraces with awn-like appendage on the glume 

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