大豆 [Glycine max (L.) Merr.] 含有丰富的不饱和脂肪酸、优质蛋白和多种微量元素，具有很高的营养价值和经济价值，是世界上很多国家重要的粮油作物。随着全球气候逐渐变暖，越来越多的国家和地区土壤缺水现象频发，干旱已经成为影响全球大豆产量和品质的重要因素之一。大豆耐旱相关性状是复杂的数量遗传性状，受多基因共同控制，至今大豆耐旱功能基因和耐旱机制方面的研究进展缓慢。定位大豆耐旱相关性状的数量性状位点（QTL），开发与其紧密连锁的分子标记，挖掘耐旱相关基因，将加快大豆耐旱分子育种进程。

本研究将传统QTL定位和QTL-seq分析相结合，挖掘大豆耐旱相关性状的QTL和候选基因；筛选出位于大豆11号染色体主效QTL区间内的耐旱候选基因Glyma.11g143500，该基因编码一个尿苷二磷酸-N-乙酰氨基葡萄糖（UDP-N-acetylglucosamine，UAA）转运蛋白；通过转基因拟南芥和大豆发状根复合体植株对该基因进行功能分析；最后根据该基因内的插入/缺失（InDel）开发了一个可用于耐旱大豆分子标记辅助选择的衍生的剪切扩增多态性序列（dCAPS）标记。主要研究结果如下：

1. 大豆重组自交系群体LM6亲本的耐旱性评价和耐旱指标筛选。对大豆重组自交系（RIL）群体LM6的母本Lin和父本Meng进行干旱处理，利用萎蔫等级（WS）、萎蔫天数（DTW）、叶片相对含水量（LRWC）、叶片相对电导率（LRC）、地上部相对鲜重（RSFW）、地上部相对干重（RSDW）、根相对鲜重（RRFW）、根相对干重（RRDW）、相对生长速率（RGR）和根冠比（R/S）10个指标进行耐旱性评价。结果表明，干旱处理后，Meng比Lin植株具有更高的DTW、LRWC、RSFW、RSDW、RRFW、RRDW和RGR值，和更小的WS和LRC值，耐旱性更强。对选取的12份耐旱性不同的大豆材料进行上述耐旱性相关指标的测定与分析，结果发现DTW是最方便测定的耐旱鉴定指标，广义遗传率高达97.61 %。各指标间的相关性分析结果表明，DTW与LRWC呈极显著（P < 0.01）正相关，而与WS和LRC均呈极显著（P < 0.01）负相关，且WS、LRC、LRWC的广义遗传率分别为95.36 %、92.65 %和96.59 %，同样适用于大豆群体的耐旱性评价。

2. 大豆重组自交系群体LM6耐旱相关性状的鉴定与QTL定位。连续三年对LM6群体进行耐旱表型鉴定，WS、DTW、LRWC和LRC的广义遗传率分别为94.51 %、95.80 %、94.86 %和94.79 %。基于复合区间作图（CIM）模型和混合复合区间作图（MCIM）模型进行QTL定位，分别检测到6个、9个、7个和9个控制WS、DTW、LRWC和LRC的QTL，其中有14个尚未被报道。在大豆第11号染色体上，上述四个指标均能检测到至少一个主效QTL（表型变异解释率大于10 %），并且这些QTL的定位区间相近或存在重叠区域，将其视为一个主效QTL簇。两种模型的定位结果均表明，该QTL簇的优异等位基因来自亲本Lin。基于CIM模型，利用WS、DTW和LRWC在2014年、2015年和2016年的表型数据以及最佳线性无偏预测（BLUP）值，分别在11号染色体上重复检测到主效QTL，即qWS-11-2、qDTW-11-2和qLRWC-11-1，表型变异解释率分别为11.1 %～38.7 %、18.1 %～45.0 %和12.2 %～39.1 %；利用LRC在2014年和2016年的表型数据以及BLUP值，均能在11号染色体上检测到qLRC-11-1，表型变异解释率为26.6 %～30.7 %。基于MCIM模型，再次检测到了qWS-11-2、qDTW-11-2、qLRWC-11-1和qLRC-11-1，表型变异解释率分别为26.4 %、30.5 %、26.1 %和23 %。比较重复检测到的QTL位置，qWS-11-2和qDTW-11-2在大豆第11号染色体上的定位区间存在重叠，其物理区间为10,924,723 bp～11,145,698 bp。该区间还位于qLRWC-11-1和qLRC-11-1定位区间内，因此，该位点是一个能够控制多个大豆耐旱相关性状的主效QTL。

3. 大豆重组自交系群体LM6耐旱相关性状的QTL-seq分析。对LM6群体的亲本Lin和Meng，以及耐旱家系DNA混池（T-Pool）和敏旱家系DNA混池（S-pool），进行DNA文库构建并重测序。基于测序数据与Glycine max Wm82参考基因组间的序列比对，开发分子标记。通过QTL-seq获得的1,263,199个高质量单核苷酸多态性（SNP）检测到大豆第11号染色体上的两个物理区间与DTW相关联，分别为9,005,039 bp～12,605,361 bp和23,015,905 bp～26,988,286 bp。利用200,380个高质量InDel，检测到与DTW关联的区域位于11号染色体9,156,701 bp～12,611,019 bp和24,680,069 bp～26,471,858 bp。两种分子标记关联到的区域基本重叠。其中，通过传统QTL定位方法检测到的qDTW-11-2位于DTW的第一个关联区域内。

4. 大豆耐旱主效QTL内重要候选基因的挖掘。针对位于大豆第11号染色体上的主效QTL簇重叠区间（10,924,723 bp～11,145,698 bp，约220 kb），利用QTL-seq数据及候选基因测序分析该区间内的序列变异位点，发现Glyma.11G143500基因编码序列（CDS）内的InDel，即InDel-1，与DTW表型显著关联。将InDel-1在整个LM6群体中进行基因分型并整合进遗传图谱中，进行QTL再次定位。结果发现InDel-1处的QTL最高可分别解释WS、DTW、LRWC和LRC表型变异的39.4 %、49.9 %、33.7 %和36.9 %，为耐旱相关性状的主效QTL。在LM6群体中，具有亲本Lin中InDel-1基因型的家系具有更大的DTW和LRWC值，及更小的WS和LRC值，表明InDel-1的耐旱优异基因型来源于亲本Lin。基因功能注释表明，Glyma.11G143500属于UAA基因家族，命名为GmUAA6。上述InDel-1变异导致GmUAA6在Lin中的蛋白序列比其在Meng中的蛋白序列多了一个赖氨酸，但并不改变其在高尔基体上的亚细胞定位。蛋白结构预测结果表明，与Meng中的GmUAA6蛋白相比，Lin中GmUAA6的蛋白二级结构中α螺旋和β转角减少，而延伸链和无规卷曲数增多，三维结构也略有不同，可能导致蛋白功能不同。

5. 大豆耐旱候选基因GmUAA6的功能分析及dCAPS标记开发。将来源于Lin的耐旱优异等位基因GmUAA6^Lin的CDS构建过表达载体，通过农杆菌介导的遗传转化法转入野生型拟南芥中，对后代纯合株系进行耐旱性鉴定试验。结果表明，干旱两周再复水4天后，野生型的存活率均值为28.13 %，而过表达GmUAA6^Lin的3个转基因拟南芥株系存活率均值分别为44.64 %、52.78 %和68.75 %，表明过表达GmUAA6^Lin的拟南芥耐旱性增强。进一步分别构建GmUAA6^Lin和GmUAA6^Meng（来源于Meng的CDS）的过表达载体并转入大豆发状根中，发现干旱处理两周后，过表达GmUAA6^Lin和GmUAA6^Meng的转基因大豆发状根复合体植株比转空载体的对照发状根复合体植株具有更高的LRWC，即植株相同部位叶片相对含水量更高，耐旱性更强；而且，过表达GmUAA6^Lin比过表达GmUAA6^Meng的大豆发状根复合体植株表现出更强的耐旱性，表明GmUAA6^Lin为耐旱优异等位基因。在GmUAA6内的InDel-1处设计特异引物，开发了一个可用于耐旱大豆分子辅助选择的dCAPS标记。该分子标记在LM6群体亲本Lin和Meng以及10份极端耐旱家系和10份极端干旱敏感家系中进行了验证。

综上所述，本研究通过传统QTL定位方法共检测到15个新的大豆耐旱相关性状QTL，并将位于11号染色体上控制多个大豆耐旱相关性状且稳定遗传的主效QTL定位到约220 kb的区间。在该区间筛选一个关键候选基因GmUAA6。通过遗传转化试验证实过表达GmUAA6优异等位基因能够增强转基因大豆发状根复合体植株和转基因拟南芥的耐旱性。基于GmUAA6内的InDel-1开发了一个可用于耐旱大豆分子辅助选择的dCAPS标记。

Soybean [Glycine max (L.) Merr.] is rich in unsaturated fatty acids, high-quality protein and a variety of essential elements, which has very high nutritional and economic value, and is an important oil crop in many countries in the world. With the gradual warming of the global climate, more and more countries and regions will suffer from frequent soil water shortages. Drought has become one of the most important factors affecting soybean yield and quality. Drought-tolerance related traits in soybean are complex quantitative genetic traits and controlled by multiple genes. So far, the research progress on functional genes and mechanisms of drought tolerance in soybean has been slow. Mapping of quantitative trait loci (QTL) for drought tolerant traits in soybean, developing molecular markers closely linked to it, and identifying drought tolerance related genes can accelerate the process of soybean drought-tolerant molecular breeding.

In present study, traditional QTL mapping and QTL-seq analysis were combined to detect QTLs and candidate genes for drought tolerance traits in soybean. Then Glyma.11g143500, which encodes a UDP-N-acetylglucosamine (UAA) transporter, was identified as a candidate gene for drought tolerance in the major QTL on soybean chromosome 11. The function of this gene was analyzed by transgenic Arabidopsis and soybean hairy root composite plants. Finally, based on the insertion/deletion (InDel) within this gene, a derived cleaved amplified polymorphic sequences (dCAPS) marker that can be used in molecular marker assisted selection of drought-tolerant soybean was developped. The main findings are as follows:

1. Evaluation of drought tolerance of the parents of soybean LM6 population and screening of drought tolerance indicators. The female parent Lin and male parent Meng of soybean recombinant inbred line (RIL) population LM6 were treated with drought, and a total of 10 indicators were used to evaluate their drought tolerance, including wilting score (WS), days-to-wilt (DTW), leaf relative water content (LRWC), leaf relative conductivity (LRC), relative shoot fresh weight (RSFW), relative shoot dry weight of (RSDW), relative root fresh weight (RRFW), relative root dry weight (RRDW), relative growth rate (RGR) and root/shoot ratio (R/S). The results showed that after drought treatment, the plants of Meng had larger DTW, LRWC, RSFW, RSDW, RRFW, RRDW and RGR, as well as smaller WS and LRC, which indicated that Meng was more drought-tolerant than Lin. The above-mentioned traits were determined and analyzed in 12 soybean accessions with different drought tolerance. The results showed that DTW was the most convenient and stable genetic indicator for drought tolerance evaluation, with the broad-sense heritability as high as 97.61 %. The correlation analysis results showed that DTW was positively correlated with LRWC (P < 0.01), and negatively correlated with WS and LRC (P < 0.01). The broad-sense heritability of WS, LRC and LRWC were 95.36 %, 92.65 % and 96.59 %, respectively. These results indicated that WS, LRWC and LRC were also suitable for the evaluation of drought tolerance of soybean.

2. QTL mapping of drought tolerance-related traits in soybean LM6 RIL population. Drought-tolerant phenotypes were determined in LM6 population for three years. The broad-sense heritability of WS, DTW, LRWC and LRC were 94.51 %, 95.80 %, 94.86 % and 94.79 %, respectively. QTL mapping was performed with the composite interval mapping (CIM) model and the mixed composite interval mapping (MCIM) model. A total of 6, 9, 7 and 9 QTLs were detected by WS, DTW, LRWC and LRC, respectively. Among them, 14 QTLs have not been reported. For each trait mentioned above, there was at least one major QTL on soybean chromosome 11 that could explain more than 10 % of phenotypic variation. These QTL locations were closely adjacent or overlapped, which could be considered as a major QTL cluster. The mapping results of both models showed that the superior allele of this QTL cluster derived from Lin parent. Through the CIM model, the major QTLs, including qWS-11-2, qDTW-11-2 and qLRWC-11-1, were repeatedly detected on soybean chromosome 11 by using the phenotypic data of each year as well as the best linear unbiased prediction (BLUP) value of WS, DTW and LRWC, which explaned 11.1-38.7 %, 18.1-45.0 % and 12.2-39.1 % of the phenotypic variation, respectively. The major QTL, qLRC-11-1, was detected on chromosome 11 by using LRC in 2014 and 2016 as well as the BLUP value, which explained 26.6 % to 30.7 % of the phenotypic variation. Based on MCIM model, qWS-11-2, qDTW-11-2, qLRWC-11-1 and qLRC-11-1 could be detected again, which explained 26.4 %, 30.5 %, 26.1 % and 23 % of the phenotypic variation, respectively. The locations of qWS-11-2 and qDTW-11-2 overlapped, with a physical interval ranged from 10,924,723 bp to 11,145,698 bp on soybean chromosome 11. This region was also located within the mapping interval of qLRWC-11-1 and qLRC-11-1, therefore, this was a major locus that could control multiple drought tolerance-related traits in soybean.

3. QTL-Seq analysis of drought-tolerance related traits in soybean LM6 RIL population. In addition to the parents of Lin and Meng, the DNA mixed pools of drought-tolerant lines (reffered as T-Pool) and drought-sensitive lines (referred as S-pool) were also used for the construction of DNA libraries and resequencing. Based on sequence alignment between the Glycine Max Wm82 reference genome and sequencing data, genome-wide molecular markers were developed. Through QTL-seq, two physical regions on soybean chromosome 11 were detected to be associated with DTW by 1,263,199 high-quality single nucleotide polymorphisms (SNPs), which were 9,005,039-12,605,361 bp and 23,015,905-26,988,286 bp, respectively. Using 200,380 high quality InDel, the DTW associated region was detected on chromosome 11 at 9,156,701-12,611,019 bp and 24,680,069-26,471,858 bp, which overlapped with the SNP detected regions. The qDTW-11-2 detected by traditional QTL mapping method was located in the first associated region of DTW.

4. Identification of candidate genes in the major QTL related to drought tolerance in soybean. Based on QTL-seq data and gene sequencing analysis, an insertion/deletion (InDel) in the coding sequence (CDS) of Glyma.11G143500, namely InDel-1, was identified in the overlapping interval (10,924,723-11,145,698 bp, about 220 kb) of the major QTL cluster on soybean chromosome 11, which showed signficant association with DTW. InDel-1 was then genotyped in the entire LM6 population and integrated into the genetic map for QTL re-mapping. The re-mapping results showed that InDel-1 was the major QTL for drought tolerance related traits, which could explain 39.4 %, 49.9 %, 33.7 % and 36.9 % of the phenotypic variation of WS, DTW, LRWC and LRC, respectively. Moreover, in LM6 population, the lines with the same InDel-1 allele as Lin had larger DTW and LRWC, and smaller WS and LRC, indicating that the superior drought-tolerant allele of InDel-1 was derived from the parent Lin. Glyma.11G143500 belongs to the UAA gene family (named GmUAA6), the above InDel-1 mutation resulted in one more lysine in the protein sequence of GmUAA6 in Lin than in Meng, but did not change the subcellular localization of GmUAA6 in Golgi. Protein structure prediction showed that compared with the GmUAA6 protein in Meng, the secondary structure of GmUAA6 in Lin decreased α helices and β turns, while the number of extended chains and random coils increased, and the three-dimensional structure of GmUAA6 in Lin and Meng was also slightly different, which might lead to different protein functions.

5. Functional analysis of drought tolerance candidate gene GmUAA6 in soybean and development of a dCAPS marker. The overexpression vector containing drought-tolerance superior gene GmUAA6^Lin (the CDS of GmUAA6 in Lin) was constructed and transferred into wild-type Arabidopsis through Agrobacterium-mediated genetic transformation. The drought tolerance of homozygous progeny lines was subsequently evaluated. The average survival rate of wild-type was 28.13 % after drought treatment for two weaks and then rehydration for four days, while the average survival rate of three transgenic Arabidopsis lines overexpressing GmUAA6^Lin were 44.64 %, 52.78 % and 68.75 %, respectively, suggesting that GmUAA6^Lin overexpression enhanced the drought tolerance of transgenic Arabidopsis. Next, the effects of two GmUAA6 alleles, GmUAA6^Lin and GmUAA6^Meng (CDS from Lin and Meng, respectively), were comapred by transgenic soybean composite plants. The result showed that after drought treatment, the transgenic soybean hairy root composite plants overexpressing GmUAA6^Lin and GmUAA6^Meng had higher LRWC than those with empty vector. Moreover, the soybean hairy root composite plants overexpressing GmUAA6^Lin showed stronger drought tolerance than that overexpressing GmUAA6^Meng, indicating that GmUAA6^Lin was the superior allele for drought tolerance. Specific primer at InDel-1 in GmUAA6 was designed to develop a dCAPS marker for molecular assisted selection breeding of drought-tolerant soybean. This molecular marker was validated in female parent Lin, male parent Meng, 10 extremely drought tolerant lines and 10 extremely drought sensitive lines of LM6 population.

In conclusion, a total of 15 novel QTLs associated with drought tolerance traits in soybean were detected in this study by traditional QTL mapping, and the major QTL on chromosome 11 was mapped to a region of about 220 kb. A key candidate gene GmUAA6 was identified from this region. Overexpression of GmUAA6 enhanced the drought tolerance of transgenic Arabidopsis and soybean hariy root composite plants. Basd on the InDel-1 within GmUAA6, a dCAPS marker was developed for molecular marker assisted selection of drought-tolerant soybean.

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