新疆稻麦子（Triticum petropavlovskyi Udacz.et Migusch.，2n=6x=42，AABBDD）是上个世纪五十年代在我国新疆发现的一种特有的栽培裸粒小麦。新疆稻麦子在形态学方面与普通六倍体小麦有较明显的区别，具体表现为长穗、长颖、长粒和高千粒重等特征。目前国内外学者对新疆稻麦子的研究主要聚焦于其起源演化过程和长颖性状的遗传分析，而对其长穗、籽粒等产量相关性状研究较少。小麦产量三要素包括千粒重、穗粒数和单位面积穗数。新疆稻麦子作为普通小麦的初级基因库，通过与普通小麦杂交可以将新疆稻麦子中与小麦产量三因素相关的优异基因转移到栽培小麦背景中，通过提高小麦的穗长、粒长和千粒重从而提高产量。因此，通过对控制新疆稻麦子的长穗、长颖等性状进行QTL定位，不仅可以挖掘新疆稻麦子的有益基因，同时对拓宽栽培小麦遗传基础及提高小麦产量都具有十分重要的意义。

本实验室前期以新疆稻麦子洛浦（T. petropavlovskyi luopu）为母本，小麦栽培品种扬麦158为父本构建了一个包含208个家系的BC2F10染色体片段置换系(Chromosome Segment Substitution Line, CSSL）群体。在此基础上，本研究通过多年多重复对该群体的两个亲本及208个家系的穗长、护颖长、外颖长、内颖长、千粒重、粒长、粒宽及长宽比这8个性状的表型数据进行调查分析；利用小麦55K SNP芯片对（新疆稻麦子×扬麦158）CSSL群体各家系进行了基因分型分析；利用55K SNP分析，构建了（新疆稻麦子×扬麦158）CSSL群体高密度的遗传图谱；利用构建的遗传图谱，结合对（新疆稻麦子×扬麦158）CSSL群体双亲以及各家系的两年多重复的表型调查数据，对新疆小麦控制穗部、籽粒性状相关QTL/基因进行了QTL定位；进一步利用构建的F2次级分离群体，对新疆小麦7A染色体短臂上的QTL簇进行了进一步定位。主要研究结果如下：

1.利用小麦55K SNP芯片对CSSL群体各家系进行基因分型分析

根据小麦55K SNP芯片，首先筛选在双亲新疆稻麦子洛浦和扬麦158之间有多态的 SNP 位点；进一步利用软件GGT2 绘制染色体片段渐渗图；根据染色体片段渐渗图分析了（新疆稻麦子×扬麦158）CSSL群体各家系基因组内渐渗SNP的数目及分布规律。根据渐渗图，发现新疆稻麦子洛浦的染色体片段基本能够覆盖（新疆稻麦子×扬麦158）CSSL群体家系的21条染色体，说明该CSSL群体可以用于进一步的QTL定位分析。

2.利用55K SNP芯片构建了（新疆稻麦子×扬麦158）CSSL群体高密度的遗传图谱

通过筛选小麦55K芯片中的SNP标记，共得到23,889个在双亲新疆稻麦子洛浦和扬麦158之间有多态的SNP标记。进一步利用IciMapping V4.1和JoinMap 4.0软件构建了覆盖新疆稻麦子洛浦21条染色体的遗传图谱。该遗传图谱共包含3,523个SNP标记，总遗传距离2,801.664 cM，平均遗传距离为0.795cM。其中A染色体组的遗传距离为878.648cM，包含1,162个SNP标记，占遗传图谱总标记数的32.98%，平均遗传距离为0.756cM；B染色体组的遗传距离为909.477cM，包含1,049个SNP标记，占遗传图谱总标记数的29.78%，平均遗传距离为0.867cM；D染色体组的遗传距离为1,013.539cM，包含1,312个SNP标记，占遗传图谱总标记数的37.24%，平均遗传距离为0.773cM。在21条染色体中，遗传距离最短的为4D染色体，为88.074 cM；遗传距离最长的为1D染色体，为210.605cM；在遗传图谱中，平均标记间的遗传距离为0.509 cM（6D）– 1.660 cM（4B）。

3.利用（新疆稻麦子×扬麦158）CSSL群体对新疆小麦控制穗部、籽粒性状相关QTL/基因进行精细定位

利用构建的遗传图谱，结合对（新疆稻麦子×扬麦158）CSSL群体双亲以及各家系的两年多重复的表型调查数据，对新疆小麦控制穗部、籽粒性状相关QTL/基因进行了QTL初步定位。定位结果共检测到与控制穗长、护颖长、外颖长、内颖长、千粒重、粒长、粒宽和长宽比8个性状相关的97个QTL，位于小麦的21条染色体上，解释表型变异的范围为0.1824% -- 53.1912%。其中有14个QTL可以在两年中被重复检测到，分别位于2B、2D、3D、4A、7A、7B和7D染色体上，控制穗长、护颖长、外颖长、内颖长、千粒重、长宽比的且稳定的QTL分别有3、5、2、2、1、1个。其中位于7A染色体短臂127.5Mb – 133.2Mb（参考中国春基因组v1.0）之间有一个同时控制穗长、护颖长、外颖长的QTL簇。

4.利用F2次级分离群体对新疆小麦7A染色体短臂上的QTL簇进行精细定位

因为7A染色体短臂127.5Mb – 133.2Mb（参考中国春基因组v1.0）之间的QTL簇对穗长、护颖长、外颖长贡献率较高，所以为了精细定位该位点，以CSSL群体中2017CY92（典型长颖家系）为母本，以扬麦158为父本构建了F2次级分离群体。参考中国春7A染色体127.5Mb – 133.2Mb的基因组序列，进一步开发SNP引物和CAPS引物，利用这些引物在包含609个单株的F2次级分离群体中进行分析。根据交换单株2019LZP859-9、2019LZP907-3等的表型和分子标记分析结果最终将控制新疆小麦穗长和颖长的QTL缩小至SNP41698和CAPS36261之间。参考中国春基因组序列，最终将该QTL定位于128.8 - 130.3Mb之间，物理距离1.5Mb。

Triticum petropavlovskyi Udacz.et Migusch. (2n=6x=42, AABBDD) is a kind of unique cultivated wheat found in Xinjiang province of China in the 1950s. It has distinctive morphological characters such as long spike, long glume, long grain and high grain weight. Up to now, researchers mainly focus on the origin and evolution of T. petropavlovskyi and the genetic analysis of long glume, but few on the analysis of the yield related characters such as long spike and grain traits. The three factors of wheat yield include 1,000 grain weight, the number of grains per spike and the number of spikes per unit area. T.petropavlovskyi is the primary germplasm of common wheat, and the excellent genes related to three factors of yeild in T.petropavlovskyi can be transferred into the background of cultivated wheat by crossing with common wheat. Therefore, QTL mapping for controlling the traits, spike- and grain-related traits of T.petropavlovskyi can not only excavate the beneficial genes of T.petropavlovskyi, but also broaden the genetic basis of cultivated wheat and improve the yield of wheat.

In this study, a BC2F10 (chromosome segment substitution line, CSSL) population derived from the cross of T. petropavlovskyi luopu and Yangmai158 was constructed and contained 208 lines. On this basis, the phenotypic data of 8 traits, including spike length, empty glume length, outer glume length, inner glume length, 1,000-grain-weight, kermel length, kernel width and kernel length/kernel width ratio, were investigated and analyzed in two parents and 208 families of this population in 2017-2018 and 2018-2019, respectively. Wheat 55K AXIOM ARRAY was used to genotype of (T. petropavlovskyi×Yangmai 158) CSSL population and constructed a high density genetic map of CSSL population. Based on the genetic map and the two-year repeated phenotypic data of their parents and families in (T. petropavlovskyi×Yangmai 158) CSSL population, the QTL/genes related to spike and grain characters in T. petropavlovskyi were located. Furthermore, the QTL clusters on the short arm of chromosome 7A of T. petropavlovskyi were fine mapped using the secondary F2 population. The main results are as follows:

1.Genotyping of CSSL population families using wheat 55K AXIOM ARRAY

According to wheat 55K AXIOM ARRAY, SNP loci with polymorphism between the T. petropavlovskyi luopu and Yangmai 158 were selected, and the chromosome segment introgression map of CSSL population was drawn using GGT2 . The number and distribution of introgressive SNPs were also analyzed in CSSL population. In the chromosome segment introgression map, the chromosome fragments of T. petropavlovskyi luopu basically covered 21 chromosomes of the CSSL population family, indicating that the CSSL population could be used for QTL mapping.

2.Construction of a high density genetic map based on (T. petropavlovskyi ×Yangmai158) CSSL population

A total of 23,889 polymorphic markers between T. petropavlovskyi luopu and Yangmai158 were obtained by selecting SNP markers in wheat 55K AXIOM ARRAY. A genetic map covering 21 chromosomes was constructed using IciMapping V4.1 and JoinMap 4.0, which contained 3,523 SNP markers. The total genetic distance was 2,801.664 cM and the average genetic distance was 0.795 cM. The genetic distance of the A genome was 878.648cM, which contained 1,162 SNP markers, accounting for 32.98% of the total number of markers in the genetic map, and the average genetic distance was 0.756cM. The genetic distance of the B genome was 909.477cM, which contained 1,049 SNP markers, accounting for 29.78% of the total number of markers in the genetic map and the average genetic distance was 0.867cM. The genetic distance of the D chromosome was 1,013.539cM, which contained 1,312 SNP markers, accounting for 37.24% of the total number of markers in the genetic map and the average genetic distance was 0.773cM. Among the 21 chromosomes, the shortest genetic distance was 4D chromosome, which was 88.074 cM. The longest genetic distance was 1D chromosome, which was 210.605 cM. The average genetic distance ranged from 0.509 cM (6D) to 1.660 cM (4B).

3.QTL mapping of spike- and grain-related traits using (T. petropavlovskyi luopu and Yangmai158 ) CSSL population.

Using the high density genetic map and the phenotypic data of the CSSL population for two years, a total of 97 QTLs controlling 8 traits including spike length, empty glume length, outer glume length, inner glume length, 1000-grain weight, kernel length, kernel width and kernel length/kernel width ratio were detected on all chromosomes of wheat, the phenotypic variance explained was from 0.1824% to 53.1912%. A total of 14 stable QTLs that 3 QTLs related to spike length, 5 QTLs related to empty glume length, 2 QTLs related to outer glume length, 2 QTLs related to inner glume length, 1 QTL related to 1,000-grain weight, and 1 QTLs related to kernel length/kernel width ratio could be repeatedly detected in two years, located at 2B、2D、3D、4A、7A、7B and 7D. Among them, a QTL cluster located between the 127.5Mb – 133.2Mb of the short arm of the 7A chromosome (referring to the Chinese spring genome v1.0) controlled spike length, empty glume length and outer glume length was detected, indicating that this region was significantly related to yield traits.

4.Fine mapping of QTL cluster in the chromosome 7AS of T. petropavlovskyi by a secondary F2 population.

    Because the QTL cluster on the short arm of chromosome 7A 127.5Mb - 133.2Mb (refer to Chinese Spring genome v1.0) had a high contribution to spike length, empty glume length and outer glume length. To fine mapping the QTL cluster, we built a F2 population derived from 2017CY92(a long glume CSSL line) and Yangmai 158. According to the sequence of 7A 127.5Mb - 133.2Mb of Chinese Spring, we developed SNP primers and CAPS primers to analysis the F2 population. According to the phenotype and molecular marker analysis of recombinant individual 2019LZP859-9 and 2019LZP907-3, etc., the QTL cluster controlling spike length, empty glume length and outer glume length of T.petropavlovskyi was finally located to the region between SNP41698 and CAPS36261.The QTL cluster was narrowed to the region between 128.8 - 130.3 Mb with a physical distance of 1.5 Mb.

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