Research progress on elongation of cooked rice
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摘要:
水稻饭粒延伸性是指米粒蒸煮时的延伸特性，用蒸煮后米粒长度增加值与蒸煮前米粒长度的比值来衡量，是评价稻米蒸煮食味品质的重要指标之一。随着现代遗传学及基因组学相关理论和育种技术的发展，人们对水稻饭粒延伸性的遗传研究也日趋深入。本文综述了影响水稻饭粒延伸性的相关因素及其遗传研究进展，指出了水稻饭粒延伸性遗传研究目前存在的主要问题，分析了水稻饭粒延伸性遗传研究的应用前景。
Abstract:Cooked rice elongation (CRE) refers to the elongation characteristics of rice grains during cooking, is evaluated by the ratio of the added value of rice grain length after cooking to the length of rice grain before cooking. It is one of the important indicators of cooking and eating quality. With the development of modern genetics and genomics related theories and breeding technology, the genetic research of CRE has also become increasingly in-depth. In this paper, the related factors affecting CRE and the main progress of genetic research on CRE were summarized, the existing problems of genetic research on CRE were also pointed out, and the prospects of genetic research on CRE were analyzed.
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苦楝Melia azedarach又名翠树、楝树、紫花树、森树等，为楝科楝属落叶乔木，分布于中国、韩国、日本、印度、斯里兰卡、印度尼西亚和澳大利亚等地，欧洲、美洲也有栽培[1].苦楝在我国分布广泛，水平分布为北纬18° ~ 40°，南至海南省崖县，北到河北保定和山西运城、陕西渭南、陇南地区，东至台湾、沿海各省，西到四川、云南保山[2].它生长速度快、木材材质优良、纹理美丽，易加工，可用于家具、建筑、农具、船舶、乐器制作等方面，木材抗白蚁、抗虫蛀、耐腐.苦楝耐烟尘，能大量吸收有毒有害气体，是优良的城市及工矿区绿化树种，也是我国南方四旁绿化常用树种[3-4].苦楝的根、皮、花、果均可入药，也可作为植物源农药[5].遗传多样性是生物多样性的重要组成部分，SRAP（Sequence-related amplified polymorphism，相关序列扩增多态性）结合了AFLP及RAPD各自的优点，方便快速，只需要极少量DNA材料，且不需要预先知道DNA序列信息，即可快速获得大量的信息，试验结果稳定可靠，且再现性较高，重复性较好[6-7].目前为止，国内对于苦楝的遗传多样性分析，鲜见开展过SRAP的研究.本试验采用单因素和正交试验设计从DNA、dNTPs、Mg2+、引物和TaqDNA聚合酶5个组分浓度对苦楝SRAP-PCR反应体系进行优化，旨在寻找一种高效、快速、经济的试验方法，建立适合苦楝的SRAP-PCR反应体系，为进一步应用SRAP技术对苦楝群体遗传多样性、种质资源鉴定等研究提供参考[7].
1. 材料与方法
1.1 材料
苦楝幼叶于2013年7月取自华南农业大学苗圃，随用随采，用于苦楝基因组DNA的提取，采集叶片分别为海南三亚、广东兴宁、广西梧州、福建建瓯、江西南昌、安徽利辛、陕西蒲城、河北邯郸种源.所用正向引物序列为Me19（TGAGTCCAAACCGGTTG）和Me27（TGGGGACAACCCGGCTT），反向引物序列为Em2（GACTGCGTACGAATTTGC）、Em4（GACTGCGTACGAATTTGA）和Em5（GACTGCGTACGAATTAAC）.
1.2 主要试剂和仪器
用于SRAP-PCR反应的Taq酶、dNTPs、Mg2+为TaKaRa公司产品，引物由北京华大基因研究中心合成，PCR反应在东胜创新生物技术有限公司的PCR扩增仪上进行，DNA浓度和纯度使用超微量紫外分光光度计（Thermo Nanodrop 2000）检测.
1.3 基因组DNA的提取
苦楝基因组DNA提取参照上海生工生物工程有限公司柱式基因组DNA提取试剂盒说明书进行.所提取的基因组DNA用8 g·L-1琼脂糖凝胶电泳检测品质，并采用超微量紫外分光光度计检测DNA的浓度和纯度，然后将DNA稀释至50 ng·μL-1，置于-20 ℃条件下保存备用.
1.4 PCR扩增
SRAP-PCR反应程序为：94 ℃预变性5 min；94 ℃变性1 min，35 ℃复性1 min，72 ℃延伸1 min，5个循环；94 ℃变性1 min，50 ℃复性1 min，72 ℃延伸1 min，30个循环；72 ℃延伸10 min.扩增产物采用20 g·L-1的琼脂糖凝胶电泳，电泳后在自动凝胶图像分析仪上拍照分析.
1.5 PCR反应体系单因素分析
对影响苦楝SRAP-PCR反应的主要因素（模板DNA、dNTPs、Mg2+、引物和Taq酶）进行单因子试验.对各影响因子分别设置8个梯度处理：模板DNA为0、10、20、30、40、50、60和70 ng；dNTPs为0、0.05、0.10、0.15、0.20、0.25、0.30和0.35 mmol · L-1；Mg2+为0、1.0、1.5、2.0、2.5、3.0、3.5和4.0 mmol·L-1；引物为0、0.16、0.24、0.32、0.40、0.48、0.56和0.64 μmol·L-1；Taq DNA聚合酶为0、0.50、0.75、1.00、1.25、1.50、1.75和2.00 U.
1.6 PCR反应体系的正交试验
在对影响苦楝SRAP-PCR反应的模板DNA、dNTPs、Mg2+、引物和Taq酶进行单因子试验后采用L16（45）正交试验设计，共16个处理，每个处理设2个重复，各因素水平见表 1.根据电泳条带的多少、清晰度及背景颜色进行打分.最优的得5分，最差的得1分，并计算每个因素在不同水平下的平均得分[8].
表 1 SRAP-PCR正交试验设计L 16（45）及试验结果Table 1. L 16(45) Orthogonal designs and results of SRAP-PCR reaction
2. 结果与分析
2.1 单因素试验分析
以SRAP-PCR反应产物电泳得到的条带数目较多且清晰为筛选原则，对反应体系中起主要作用的5个因素进行单因素浓度梯度筛选试验[9-12]，每个因素设置8个浓度梯度.试验结果表明：在25 μL反应体系中，模板DNA为25 ~ 40 ng、dNTPs为0.125 ~ 0.200 mmol·L-1、Mg2+为1.75 ~ 2.25 mmol·L-1、引物为0.40 ~ 0.52 μmol·L-1、Taq DNA聚合酶为0.50 ~ 1.25 U时扩增效果好，条带较多且清晰，故将其选为后续正交试验的适宜浓度范围.
2.2 苦楝SRAP-PCR正交反应体系的优化
以上述单因素试验确定的各因素适宜浓度范围为基础，采用L 16（45）正交设计对SRAP-PCR反应体系进行优化（表 1），并根据电泳条带的多少、清晰度及背景颜色（图 1）对16个处理进行打分，打分结果如表 1所示，从2次的得分来看，重复间差异不大，试验的一致性较好，其中处理5、处理7、处理8和处理9效果较好，评分均为4分，而处理15效果不好，评分仅为1.0分.从图 2可见，模板DNA 30 ng、dNTPs 0.125 mmol·L-1、Mg2+ 2.25 mmol·L-1、引物0.48 μmol·L-1、Taq DNA聚合酶0.75 U、反应总体积25 μL时得分较高，实现最佳扩增，确定为最优组合.
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图 1 SRAP-PCR反应体系正交试验结果M：DNA maker DL2000；1 ~ 16：处理1 ~ 16（陕西蒲城种源）.Figure 1. Amplified patterns of the SRAP-PCR based on orthogonal design![]()
图 2 模板DNA、dNTPs、Mg2+、引物、Taq DNA聚合酶与平均得分的关系Figure 2. Relationship between concentrations and mean scores of template DNA, dNTPs, Mg2+, primer and Taq polymerase2.3 苦楝SRAP-PCR反应体系稳定性的检测
为了验证体系的准确性，以来自海南三亚、广东兴宁、广西梧州、福建建瓯、江西南昌、安徽利辛、陕西蒲城、河北邯郸的8个苦楝种源DNA为模板，选取引物Me27/Em2、Me27/Em4进行SRAP-PCR验证，其结果如图 3所示，每个种源对每个引物均有清晰的条带，且不同种源间条带有差异.由此可见，本试验建立的SRAP-PCR体系稳定可靠，适用于苦楝后续的SRAP分析.
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图 3 SRAP-PCR反应体系稳定性检测M：DNA maker DL2000；1 ~ 8：引物Me27/Em2；9 ~ 16：引物Me27/Em4；自1和9开始，从左到右依次为海南三亚、广东兴宁、广西梧州、福建建瓯、江西南昌、安徽利辛、陕西蒲城、河北邯郸种源DNA.Figure 3. The verification of Melia azedarach SRAP-PCR reaction system3. 结论
本试验建立并优化了适应苦楝SRAP-PCR的反应体系，前期对苦楝模板DNA、Mg2+、引物和Taq酶进行单因子试验，研究发现，SRAP对苦楝DNA浓度的要求不高，有一个较宽的浓度适宜范围，在25 μL体系中，模板DNA为10 ~ 70 ng时都扩增出了较清晰、带型基本相同的谱带；dNTPs设计的8个浓度梯度中，0.1 ~ 0.2 mmol·L-1范围内能扩增出清晰谱带，且条带基本相同，浓度低于0.1 mmol·L-1时，扩增条带弥散，高于0.2 mmol·L-1时，出现条带丢失的现象；Mg2+为2.00 mmol·L-1左右时扩增条带较清晰且数量多；引物介于0.48 ~ 0.64 μmol·L-1之间均能产生较为清晰的条带，且带型基本上保持一致，条带数并没有随着浓度的增加而增加；Taq DNA聚合酶用量在0.50 ~ 2.0 U范围内均可以得到清晰的带型，对其用量要求不高.进一步对苦楝SRAP-PCR的反应体系进行正交试验，并根据电泳条带的多少、清晰度及背景颜色对16个处理进行打分，从2次的得分来看，重复间差异不大，试验的一致性较好，其中处理5、处理7、处理8和处理9效果较好，评分均为4.0分，而处理15效果不好，评分仅为1.0分.根据得分可知，在25 μL反应体系中，当模板DNA 30 ng、dNTPs 0.125 mmol·L-1、Mg2+ 2.25 mmol·L-1、引物0.48 μmol·L-1、Taq DNA聚合酶0.75 U时，实现最佳扩增，确定为最优组合.以来自海南三亚、广东兴宁、广西梧州、福建建瓯、江西南昌、安徽利辛、陕西蒲城、河北邯郸的8个苦楝种源DNA为模板，选取引物Me27/Em2、Me27/Em4进行SRAP-PCR反应体系稳定性验证，结果表明，筛选体系能很好地满足苦楝基因组SRAP-PCR扩增的要求且不同种源间条带有差异.
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图 2 部分已鉴定的水稻饭粒延伸性QTLs
Chr.：染色体；黑色、红色和绿色条块分别代表饭粒延伸性、饭粒伸长率和米粒延伸指数的QTL，条块位置代表QTL的估计位置；蓝色为已克隆淀粉相关基因的物理位置
Figure 2. Partial identified QTLs for cooked rice elongation
Chr.: Chromosome; The bars in black, red, and green represent QTLs for cooked rice elongation, cooked rice elongation rate, and rice grain elongation index, respectively, the location of the bar represents the estimated location of the QTL; Blue is the physical location of the cloned starch-related genes
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