,1,2, 王强林3, 宋威武4, 黄维1, 肖桂林1, 吴承金4, 顾钦2, 宋波涛,1,*Association analysis of dormancy QTL in tetraploid potato via candidate gene markers
LI Jing-Cai,1,2, WANG Qiang-Lin3, SONG Wei-Wu4, HUANG Wei1, XIAO Gui-Lin1, WU Cheng-Jin4, GU Qin2, SONG Bo-Tao,1,*通讯作者:
收稿日期:2019-12-18接受日期:2020-03-24网络出版日期:2020-09-12
| 基金资助: |
Received:2019-12-18Accepted:2020-03-24Online:2020-09-12
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李竟才, 王强林, 宋威武, 黄维, 肖桂林, 吴承金, 顾钦, 宋波涛. 基于侯选基因标记的四倍体马铃薯休眠QTL关联分析[J]. 作物学报, 2020, 46(9): 1380-1387. doi:10.3724/SP.J.1006.2020.94200
LI Jing-Cai, WANG Qiang-Lin, SONG Wei-Wu, HUANG Wei, XIAO Gui-Lin, WU Cheng-Jin, GU Qin, SONG Bo-Tao.
休眠期是马铃薯(Solanum tuberosum L.)重要的块茎性状之一, 对于马铃薯的种植、产量、贮运和加工品质等都极为重要[1,2]。寻找调控马铃薯块茎休眠的关键基因, 揭示其分子机制, 进而准确控制休眠期, 以选育具有适宜休眠期长度的马铃薯品种, 是一种比较经济和安全的策略, 对于解决当前马铃薯产业中过长或过短休眠期带来的经济损失和食品安全隐患等问题十分关键。马铃薯块茎休眠期是一种典型的数量性状[3], 而QTL (quantitative trait locus)定位分析是寻找调控休眠的关键基因, 揭示其复杂的分子机制的适宜方法。迄今为止, 相关研究已利用连锁分析(linkage analysis)定位了20多个马铃薯块茎休眠QTL[4,5,6,7,8,9], 但这些休眠QTL的定位仅根据1~2个环境的表型数据, 无法确保其稳定性和准确性, 使得这些QTL在块茎休眠分子机制研究和马铃薯育种当中的利用受到限制。Li等[10]根据二倍体马铃薯群体EB在7个环境中的休眠期表型数据, 定位了6个加性QTL, 其中2个稳定的主效QTL, 即DorE4.6和DorB5.3, 在多个环境中显著, 分别解释表型变异的14.3%和13.9%。这些休眠QTL为马铃薯块茎休眠分子机制研究和马铃薯休眠期育种提供了重要线索。
与基于2个亲本杂交所得群体的连锁分析不同, 关联分析(association analysis)可以利用自然群体中不同基因座等位基因间的连锁不平衡(linkage disequilibrium)关系, 进行标记与性状间的相关性分析。关联分析已广泛地应用于玉米[11,12]、油菜[13]、水稻[14]、马铃薯[15,16,17,18]等作物的QTL定位, 但关于马铃薯块茎休眠QTL定位的关联分析则未见报道。为了直接在育种所用的四倍体马铃薯材料中验证Li等[10]定位的休眠QTL, 本研究拟在四倍体马铃薯自然群体St-hzau中进行关联分析以定位马铃薯块茎休眠QTL: 参考Li等[18]的研究策略, 采用基于候选基因标记的方法, 利用与休眠QTL[10]紧密连锁的候选基因标记在群体St-hzau所包含的59份四倍体马铃薯育种材料中进行关联分析, 寻找与休眠期关联的自然变异, 为聚焦控制马铃薯块茎休眠的关键基因和揭示块茎休眠分子机制奠定基础, 为马铃薯休眠期育种提供用于辅助选择的分子标记和用于改良的基因资源。
1 材料与方法
1.1 植物材料
关联群体St-hzau包含St-hzau01~59共59份四倍体马铃薯植物材料, 由农业农村部马铃薯生物学与生物技术重点实验室(华中农业大学)提供。群体St-hzau具有广泛的遗传背景, 包含S. tuberosum、S. berthaultii、S. phureja、S. vernei等血缘的马铃薯种质资源, 以及华薯3号、中薯5号、Shepody、Atlantic等常规品种。1.2 马铃薯块茎休眠期评价
将四倍体马铃薯关联群体St-hzau的植物材料于2015年种植于武汉(30.5°N, 114.4°E)、2016年种植于武汉和长阳(30.4°N, 110.7°E)的露地(种植和收获日期如表1所示), 随机区组设计, 3次重复, 每小区种植一种四倍体马铃薯材料(即一种基因型)的10个植株。遵循当地常规马铃薯生产栽培管理方法, 以确保马铃薯植株正常生长。马铃薯植株成熟后, 从3个环境中(如表1所示)的每一个小区收获15个健康的块茎, 并在25℃室温下保存7 d, 直到块茎外皮干燥, 然后在黑暗中以(20±1)℃恒温储存。每4 d观察统计一次15个块茎的发芽情况, 直到所有块茎长出至少2 mm的芽[19,20]。块茎收获至观察到80%块茎发芽(每组15个块茎中有12个发芽)的天数计为休眠期。用SPSS 22.0进行相关统计分析。Table 1
表1
表13个环境中马铃薯关联群体St-hzau种植和收获日期
Table 1
| 环境 Environment | 地点 Location | 种植日期 Planting date | 收获日期 Harvest date |
|---|---|---|---|
| I | 武汉Wuhan | 2015-01-15 | 2015-05-20 |
| II | 武汉Wuhan | 2016-01-22 | 2016-06-04 |
| III | 长阳Changyang | 2016-03-10 | 2016-07-20 |
新窗口打开|下载CSV
1.3 候选基因标记检测
取上述关联群体St-hzau所有59份马铃薯试管苗的幼嫩叶片, 采用改良的CTAB法[21]提取基因组DNA, 用于标记检测。根据Li等[10]的研究, 选择与DorB5.3等6个休眠QTL连锁的标记(标记信息如表2所示), 参考Li等[22]和Xiao等[23]的方法进行PCR扩增, PCR产物电泳检测参考Han等[24]的银染法。利用Quantity One Version 4.6.2 (Bio-Rad凝胶成像系统Universal Hood II内置软件)对电泳胶片分析读取标记条带, 并利用其中的Point-to-point semi-log回归模型根据分子量标准ΦX174 Hae III digest (NEB) 估计标记条带片段大小(Base pair)。
Table 2
表2
表2候选基因标记引物
Table 2
| 引物名称a Primer name a | 染色体 Chr. | 连锁QTL Linked QTL | 上游引物 Forward primer (5°-3°) | 下游引物 Reverse primer (5°-3°) | 退火温度 Annealing temperature (℃) |
|---|---|---|---|---|---|
| S199 | Chr05 | DorB5.3 | TGCCTACTGCCCAAAACATT | ACTGGCTGGGAAGCATACAC | 55 |
| GWD | Chr05 | DorB5.3 | TCCATCCTGAGACTGGAGATAC | ACTTGTACTGCAGGACTGGAAG | 60 |
| G6pt | Chr05 | DorB5.3 | GGCTCACACAATTGGTCATGTG | CCAAGATTGCAATAGCAGCACC | 60 |
| s1939 | Chr05 | DorB5.3 | TGAGATACTTTGTGTGCTCC | AAATTGGTTTTCCAGATTGA | 56 |
| STI058 | Chr05 | DorB5.3 | CAAGCACGTTACAACAAGCAA | TTGAAGCATCACATACACAAACA | 60-54 |
| FK | Chr06 | DorB6.3 | GCTTTGGCGTTCGTGACTCTAC | AGTGGTGTCAACAGTCTTCACG | 60 |
| S1711 | Chr06 | DorE6.17 | TTCTTCAGGGTCCTCTTTCGG | AGTGCTTCCTCGCATGGGATT | 67 |
| S1614 | Chr06 | DorE6.17, DorE6.19 | TCGTGGGTCAAGGTTGTTCAT | ATGGTGGATTAGACCTAGTTGCTG | 65 |
| Dpe-P | Chr04 | DorE4.6 | CACTACTTTTCAATCTCCTATCCC | GCATAGTCACGAACTTTTTTCC | 56 |
| α-Glu | Chr04 | DorE4.6 | ACCAAGCTGTGGTTAACCAGAG | GCAGTTGCGAATAACTGTGGCA | 60 |
| Ppe | Chr03 | DorB3.17 | TCCGTCCATCCTTTCTGCTAAC | AACTCCACCATCAACTTCAATC | 57 |
新窗口打开|下载CSV
1.4 关联分析
将上述关联群体St-hzau的标记数据输入Structure 2.3.4 [25], 将不作数迭代 (Length of Burnin Period)和其后的MCMC迭代(Number of MCMC Reps after Burnin)均设为100,000次, 选用混群模型(Admixture Model), 将群体数目(K)设为2~20, 迭代次数(Number of Iterations)设为3, 计算每个K值对应的后验概率ln P(D), 然后依据后验概率最大的原则, 利用在线软件Structure Harvester[26]选取一个合适的K值, 对应此K值的59份四倍体马铃薯的Q值用于关联分析。用TASSEL 5软件[27] (
参考Xiao等[23]和Li等[10]的结果, 用MapChart 2.2[29]绘制候选基因标记和休眠QTL位置关系图。
2 结果与分析
2.1 马铃薯块茎休眠期表型分布
从表1所列I、II和III三个田间环境中收获马铃薯关联群体St-hzau的块茎进行休眠期表型评价表明, 块茎休眠期的偏度为0.077~0.382, 峰度为-0.783~0.843 (表3), 表型数据为近正态分布(图1), 群体St-hzau的块茎休眠期属于数量性状。图1
新窗口打开|下载原图ZIP|生成PPT图1关联群体St-hzau马铃薯块茎休眠期表型分布
图中I、II和III分别对应于
Fig. 1Phenotypic distributions of potato tuber dormancy in the association population St-hzau
In the figure, I, II, and III correspond to the three field environments listed in
Table 3
表3
表33个环境中马铃薯块茎休眠期
Table 3
| 环境a Environment a | 块茎发芽起始日期 First sprouting date | 平均值 Mean | 标准差 Standard deviation | 方差 Variance | 偏度 Skewness | 峰度 Kurtosis |
|---|---|---|---|---|---|---|
| I | 2015-07-01 | 86.413 | 21.032 | 432.721 | 0.077 | 0.843 |
| II | 2016-07-10 | 68.000 | 12.000 | 134.400 | 0.181 | -0.783 |
| III | 2016-08-26 | 85.963 | 15.647 | 240.295 | 0.382 | -0.456 |
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2.2 群体结构
将关联群体St-hzau标记数据在Structure 2.3.4中的运行结果文件输入在线软件Structure Harvester选取合适的K值3, 即59份四倍体马铃薯材料可以按Structure Harvester软件的建议划分为3个亚群体, 其中St-hzau14、St-hzau27、St-hzau28、St-hzau33、St-hzau34、St-hzau35、St-hzau43、St-hzau45、St-hzau51、St-hzau52、St-hzau55、St-hzau56和St-hzau57共13份材料属于同一个亚群体A, St-hzau05、St-hzau07、St-hzau08、St-hzau13、St-hzau18、St-hzau19、St-hzau20、St-hzau21、St-hzau24、St-hzau25、St-hzau26、St-hzau38、St-hzau46和St-hzau54共14份材料属于同一个亚群体B, St-hzau01、St-hzau02、St-hzau03、St-hzau04、St-hzau06、St-hzau09、St-hzau10、St-hzau11、St-hzau12、St-hzau15、St-hzau16、St-hzau17、St-hzau22、St-hzau23、St-hzau29、St-hzau30、St-hzau31、St-hzau32、St-hzau36、St-hzau37、St-hzau39、St-hzau40、St-hzau41、St-hzau42、St-hzau44、St-hzau47、St-hzau48、St-hzau49、St-hzau50、St-hzau53、St-hzau58和St-hzau59共32份材料属于同一个亚群体C (图2)。对应K=3的59份四倍体马铃薯的Q值用于关联分析。图2
新窗口打开|下载原图ZIP|生成PPT图2St-hzau群体结构
关联群体St-hzau划分为A、B和C三个亚群体。
Fig. 2Population structure of St-hzau
The association population St-hzau was divided into three sub-populations.
2.3 与马铃薯块茎休眠期关联的候选基因标记
根据作者前期二倍体马铃薯块茎休眠研究基础, 本研究选择了11对与休眠QTL连锁的标记引物(表2), 在关联群体St-hzau中扩增出62个多态性标记带型, 其中20个已经在前期研究中被定位于二倍体马铃薯遗传连锁图上(图3), 另42个是在四倍体马铃薯关联群体St-hzau中新扩增出的多态性标记带型。图3
新窗口打开|下载原图ZIP|生成PPT图3候选基因标记与马铃薯块茎休眠QTL
第1个连锁群顶部的Chr04E表示母本ED25 (E)的4号染色体, Chr03B表示父本S. berthaultii acc CW2-1 (B)的3号染色体。最左边连锁群标尺的单位是cM。无休眠QTL的其他染色体此处省略, 详见Xiao等[23]的研究。标记位于连锁群的右侧, 休眠QTL的位置在连锁群的左侧。[*]突出显示chr05B上在马铃薯关联群体St-hzau中与块茎休眠期有显著关联的标记, 其他候选基因标记下画线标出。
Fig. 3Candidate gene markers and potato tuber dormancy QTL
Chr04E on the top of the first group indicates chromosome 4 of the maternal parent ED25 (E) and Chr03B indicates chromosome 3 of the paternal parent S. berthaultii acc. CW2-1 (B). The unit of the scale on the far left is cM for linkage groups. Chromosomes without dormancy QTL were omitted and they could be found in the research of Xiao et al. [23] The markers are on the right and locations of dormancy QTLs are on the left of the groups. Significant markers on Chr05B associated with tuber dormancy in potato association population St-hzau are highlighted by [*]. Other candidate gene markers are underlined.
MLM分析表明, 62个标记中, 定位于二倍体马铃薯5号染色体(chr05B)上与休眠QTL DorB5.3连锁的候选基因标记S199_300 (“S199”为表2中候选基因标记引物名称, “300”为利用Quantity One估计的标记片段大小300 base pairs)和GWD与马铃薯块茎休眠期具有显著的关联(P<0.05), 分别解释了马铃薯块茎休眠期表型变异的7.8%和3.2%, 分别能增加休眠期7.1 d和4.5 d。而DPe-P_250 (定位于染色体Chr04E)、α-Glu_600(Chr04E)、S1614_ 580(Chr06E)、S1711_191(Chr06E)、S1614_ 400(Chr06E)、Fk_570 (Chr06E)、Ppe_700(Chr03B)、S199_130(Chr05B)、S1939_460(Chr05B)、G6pt_465(Chr05B)、StI058_100 (Chr05B)、Fk_570(Chr06B)、Fk_590(Chr06B)在二倍体马铃薯中与休眠QTL连锁的候选基因标记, 在关联群体St-hzau中与马铃薯块茎休眠期无显著的关联(图3)。FK_1500、FK_1550、FK_1600、FK_1650、G6pt_1128、G6pt_1353、G6pt_1490、G6pt_1733、G6pt_2165、G6pt_2228、G6pt_2303、G6pt_2373、GWD_1655、GWD_1955、GWD_2055、GWD_2125、GWD_2195、GWD_1178、GWD_1378、GWD_1403、Indel_578、S1614_360、S1614_450、S1711_150、S1711_160、S1711_180、S1711_285、S1711_310、S1711_350、S1711_390、S1711_460、S1711_480、S1711_530、S1711_560、S1711_590、s1939_295、s199_118、S711_320、STI058_108、STI058_114、STI058_92、STI058_95共42个在关联群体St-hzau中新扩增出的多态性标记与马铃薯块茎休眠期均无显著的关联。
3 讨论
3.1 候选基因标记
根据前期基础, 本研究选择了11对与休眠QTL连锁的标记引物, 在关联群体St-hzau中扩增出62个多态性标记带型, 其中20个已经被Li等[10]定位于二倍体马铃薯中的标记, 也能在四倍体马铃薯关联群体St-hzau中检测出多态性, 充分说明了本研究所选候选基因标记的可重复性。但这20个候选基因标记中, 只有S199_300和GWD2, 即与二倍体马铃薯休眠QTL DorB5.3连锁的标记, 在四倍体马铃薯关联群体St-hzau中与块茎休眠期具有显著的关联, 其比例(10%)远低于Li等[18]所报道的马铃薯关联分析中显著的候选基因标记的比例(44%)。其原因可能是本研究所分析的与候选基因标记连锁的休眠QTL效应较小, 在二倍体连锁群体中只能解释表型变异的8.0%~14.3%[10], 在四倍体群体St-hzau中能解释的表型变异不超过7.8%, 所以易受环境效应掩盖, 不易检测到显著的关联性。而Li等[18]所报道的马铃薯淀粉含量等QTL效应较大, 可以解释表型变异的26.1%~54.9%, 所以更容易检测到显著的关联。尽管如此, 本研究结果仍然表明候选基因标记策略在马铃薯块茎休眠QTL关联分析中是一种有效的策略。3.2 休眠QTL的验证
前期研究在二倍体马铃薯连锁群体EB内定位的6个加性QTL中[10], 稳定的主效QTL DorB5.3在四倍体马铃薯关联群体St-hzau中仍然表现出与休眠期表型显著的关联, DorB5.3的稳定性在四倍体马铃薯关联群体中得到了验证, 而且与之连锁的2个候选基因标记, 即S199_300和GWD, 均表现显著。关于马铃薯块茎休眠QTL定位的关联分析未见前人报道, 而通过连锁分析, Bisognin等[4]、Freyre等[5]、Sliwka等[7]和Van den Berg等[9]在二倍体马铃薯5号染色体上分别定位了3、1、1和1个块茎休眠QTL, 其中Bisognin等[4]定位的位于标记chr05_5.9_c2_47663附近的QTL解释了块茎休眠期表型变异的15.3%, 与本研究中的主效QTL DorB5.3位置相近。但由于Bisognin等[4]所用标记全部为SNP (Single Nucleotide Polymorphism)标记, 而本研究所用标记为AFLP (Amplified Fragment Length Polymorphism)和基于PCR (Polymerase Chain Reaction)的候选基因标记, 因此缺乏共同标记(Common marker), 不能断定chr05_5.9_c2_47663附近的QTL与本研究定位的DorB5.3是否确实为同一个QTL。
关联群体St-hzau包含的马铃薯种质具有育种中常用的S. tuberosum、S. berthaultii、S. phureja、S. vernei等血缘以及常规品种华薯3号、中薯5号、Shepody、Atlantic等, 因此, 相对于前人仅在连锁群体中定位的休眠QTL [4,5,6,7,8,9], DorB5.3具有重要的育种意义, 可以作为控制休眠的基因资源直接进入育种程序, 与之连锁的候选基因标记S199_300和GWD也可以用作育种的辅助选择标记。
3.3 休眠QTL与低温糖化QTL的共定位
马铃薯块茎休眠QTL DorB5.3与Xiao等[23]定位的马铃薯还原糖含量QTL REC_B_05-1位置一致。Suttle等[30]研究表明, 马铃薯块茎休眠的解除和萌芽生长的开始伴随着许多变化, 其中就包括还原糖含量的增加。Vreugdenhil[31]也证明改变碳水化合物代谢影响马铃薯块茎休眠和发芽。Hou等[32]证明α-淀粉酶基因StAmy23参与了马铃薯块茎还原糖含量和休眠的调节, RNA干涉(RNA interference, RNAi) StAmy23导致马铃薯低温贮藏块茎中可溶性糖原含量显著增加, 还原糖含量降低, 同时使块茎萌芽延迟1~2周。与休眠QTL DorB5.3连锁的GWD是根据葡聚糖水双激酶(α-glucan water dikinase)基因开发的候选基因标记[23], 葡聚糖水双激酶在淀粉降解[33,34]及马铃薯块茎还原糖含量调节[35]中发挥着非常重要的作用, 据此推测葡聚糖水双激酶可能在控制还原糖含量和块茎休眠的过程中均发挥了作用, 马铃薯块茎休眠机制与还原糖含量变化机制可能存在着部分交叉。4 结论
本研究在四倍体马铃薯关联群体中验证了前期二倍体连锁群体中的休眠QTL定位结果, 表明候选基因标记策略在马铃薯块茎休眠QTL关联分析中是一种有效的策略; 主效QTL DorB5.3及相关标记可以直接用于马铃薯休眠育种; 葡聚糖水双激酶可能在控制还原糖含量和块茎休眠2个方面均发挥作用, 马铃薯块茎休眠机制与还原糖含量变化机制可能存在着部分交叉。参考文献 原文顺序
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DOI:10.1016/s1369-5266(01)00219-9URLPMID:11788305 [本文引用: 1]
Seed dormancy and germination are complex adaptive traits of higher plants that are influenced by a large number of genes and environmental factors. Studies of genetics and physiology have shown the important roles of the plant hormones abscisic acid and gibberellin in the regulation of dormancy and germination. More recently, the use of quantitative genetics and mutant approaches has allowed the further genetic dissection of these traits and the identification of previously unknown components. Molecular techniques, and especially expression studies and transcriptome and proteome analyses, are novel tools for the analysis of seed dormancy and germination. These tools preferentially use Arabidopsis thaliana because of the molecular genetic resources available for this species. However, Solanaceae and cereals also provide important models for dormancy research.
DOI:10.1007/s12230-018-9638-0URL [本文引用: 5]
DOI:10.1007/BF00225383URLPMID:24177897 [本文引用: 3]
Quantitative trait locus (QTL) analysis for tuber dormancy was performed in a diploid potato population (TRP133) consisting of 110 individuals. The female parent was a hybrid between haploid S. tuberosum (2x) and S. chacoense, while the male parent was a S. phureja clone. The population was characterized for ten isozyme loci, 44 restriction fragment length polymorphisms (RFLPs) and 63 random amplified polymorphic DNAs (RAPDs). Eighty-seven of these loci segregating from the female parent were utilized to develop a linkage map that comprised 10 of the 12 chromosomes in the genome. Dormancy, as measured by days-to-sprouting after harvest, ranged from 10 to 90 days, with a mean of 19 days. QTLs were mapped by conducting one-way analyses of variance for each marker locus by dormancy combination. Twenty-two markers had a significant association with dormancy, identifying six putative QTLs localized on each of chromosomes 2, 3, 4, 5, 7 and 8. The QTL with the strongest effect on dormancy was detected on chromosome 7. A multilocus model was developed using the locus with highest R(2) value in each QTL. This model explained 57.5% of the phenotypic variation for dormancy. Seven percent of possible epistatic interactions among significant markers were significant when tested through two-way analyses of variance. When these were included in the main-effects model, it explained 72.1% of the phenotypic variation for dormancy. QTL analysis in potato, the methodology to transfer traits and interactions into the 4x level, and QTLs of value for marker-assisted selection, are discussed.
DOI:10.1242/bio.039362URLPMID:30404898 [本文引用: 2]
Control of gene expression at the translation level is increasingly regarded as a key feature in many biological processes. Simple, inexpensive and reliable procedures to visualize sites of protein production are required to allow observation of the spatiotemporal patterns of mRNA translation at subcellular resolution. We present a method, named SPoT (for Subcellular Patterns of Translation), developed upon the original TimeStamp technique ( Lin et al., 2008), consisting in the expression of a fluorescent protein fused to a tagged, self-cleavable protease domain. The addition of a cell-permeable protease inhibitor instantly stabilizes newly produced tagged protein allowing us to distinguish recently synthesized proteins from pre-existing ones. After a brief protease inhibitor treatment, the ratio of tagged versus non-tagged forms is highest at sites where proteins are the most recent, i.e. sites of synthesis. Therefore, by comparing tagged and non-tagged proteins it is possible to spotlight sites of translation. By specifically expressing the SPoT cassette in neurons of transgenic zebrafish embryos, we reveal sites of neuronal protein synthesis in diverse cellular compartments during early development.
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DOI:10.1104/pp.115.4.1453URLPMID:12223876 [本文引用: 2]
In previous studies polygene mapping of a backcross population derived from haploid potato (Solanum tuberosum) and a diploid wild species (Solanum berthaultii) showed at least eight quantitative trait loci (QTLs) associated with tuber dormancy. The same population was mapped for abscisic acid (ABA) content in tubers so that any QTLs identified could be compared with those detected previously. At least three distinct loci on three chromosomes (2, 4, and 7) were associated with variation in ABA content. One of the QTLs was detected only as a main (single locus) effect, and two QTLs were found through two-locus interaction analysis (epistasis). Interaction between QTLs at markers TG234 (chromosome 2) and TG155 (chromosome 4) explained 20% of total phenotypic variance for this trait. The interaction closely resembled one previously detected for dormancy, suggesting an association between high ABA content and long tuber dormancy. Although relationships between ABA level and dormancy could be demonstrated through polygene mapping, there was no indication of a relationship between these traits when they were subjected to a conventional correlation test. This illustrates the usefulness of polygene mapping as a tool to identify possible associations between hormone levels and plant development.
DOI:10.1007/BF00223171URLPMID:24162286 [本文引用: 3]
The potential loss of chemical sprout inhibitors because of public concern over the use of pesticides underscores the desirability of breeding for long dormancy of potato (Solanum tuberosum L.) tubers. Quantitative trait locus (QTL) analyses were performed in reciprocal backcrosses between S. tuberosum and S. berthaultii toward defining the complexity of dormancy. S. berthaultii is a wild Bolivian species characterized by a short-day requirement for tuberization, long tuber dormancy, and resistance to several insect pests. RFLP alleles segregating from the recurrent parents as well as from the interspecific hybrid were monitored in two segregating progenies. We detected QTLs on nine chromosomes that affected tuber dormancy, either alone or through epistatic interactions. Alleles from the wild parent promoted dormancy, with the largest effect at a QTL on chromosome 2. Long dormancy appeared to be recessive in the backcross to S. berthaultii (BCB). In BCB the additive effects of dormancy QTLs accounted for 48% of the measured phenotypic variance, and adding epistatic effects to the model explained only 4% more. In contrast, additive effects explained only 16% of the variance in the backcross to S. tuberosum (BCT), and an additional 24% was explained by the inclusion of epistatic effects. In BCB variation at all QTLs detected was associated with RFLP alleles segregating from the hybrid parent; in BCT all QTLs except for two found through epistasis were detected through RFLP alleles segregating from the recurrent parent. At least three dormancy QTLs mapped to markers previously found to be associated with tuberization in these crosses.
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DOI:10.1038/90135URLPMID:11431702 [本文引用: 1]
Historically, association tests have been used extensively in medical genetics, but have had virtually no application in plant genetics. One obstacle to their application is the structured populations often found in crop plants, which may lead to nonfunctional, spurious associations. In this study, statistical methods to account for population structure were extended for use with quantitative variation and applied to our evaluation of maize flowering time. Mutagenesis and quantitative trait locus (QTL) studies suggested that the maize gene Dwarf8 might affect the quantitative variation of maize flowering time and plant height. The wheat orthologs of this gene contributed to the increased yields seen in the 'Green Revolution' varieties. We used association approaches to evaluate Dwarf8 sequence polymorphisms from 92 maize inbred lines. Population structure was estimated using a Bayesian analysis of 141 simple sequence repeat (SSR) loci. Our results indicate that a suite of polymorphisms associate with differences in flowering time, which include a deletion that may alter a key domain in the coding region. The distribution of nonsynonymous polymorphisms suggests that Dwarf8 has been a target of selection.
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DOI:10.1186/s12863-019-0729-9URLPMID:30885119 [本文引用: 1]
BACKGROUND: The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. The aim of the current research is to identify genomic SNPs associated with starch phosphorylation by carrying out a genome-wide association study in potatoes. RESULTS: A total of 90 S. tuberosum L. varieties were used for phenotyping and genotyping. The phosphorus content of starch in 90 potato cultivars was measured and then statistically analysed. Principal component analysis (PCA) revealed that the third and eighth principal components appeared to be sensitive to variation in phosphorus content (p = 0.0005 and p = 0.002, respectively). PC3 showed the correlation of starch phosphorus content with allelic variations responsible for higher phosphorylation levels, found in four varieties. Similarly, PC8 indicated that hybrid 785/8-5 carried an allele associated with high phosphorus content, while the Impala and Red Scarlet varieties carried alleles for low phosphorus content. Genotyping was carried out using an Illumina 22 K SNP potato array. A total of 15,214 scorable SNPs (71.7% success rate) was revealed. GWAS mapping plots were obtained using TASSEL based on several statistical models, including general linear models (GLMs), with and without accounting for population structure, as well as MLM. A total of 17 significant SNPs was identified for phosphorus content in potato starch, 14 of which are assigned to 8 genomic regions on chromosomes 1, 4, 5, 7, 8, 10, and 11. Most of the SNPs identified belong to protein coding regions; however, their allelic variation was not associated with changes in protein structure or function. CONCLUSIONS: A total of 8 novel genomic regions possibly associated with starch phosphorylation on potato chromosomes 1, 4, 5, 7, 8, 10, and 11 was revealed. Further validation of the SNPs identified and the analysis of the surrounding genomic regions for candidate genes will allow better understanding of starch phosphorylation biochemistry. The most indicative SNPs may be useful for developing diagnostic markers to accelerate the breeding of potatoes with predetermined levels of starch phosphorylation.
DOI:10.1007/s11032-019-1070-8URL [本文引用: 1]
DOI:10.1007/s00122-008-0746-yURL [本文引用: 4]
Complex characters of plants such as starch and sugar content of seeds, fruits, tubers and roots are controlled by multiple genetic and environmental factors. Understanding their molecular basis will facilitate diagnosis and combination of superior alleles in crop improvement programs (“precision breeding”). Association genetics based on candidate genes is one approach toward this goal. Tetraploid potato varieties and breeding clones related by descent were evaluated for 2 years for chip quality before and after cold storage, tuber starch content, yield and starch yield. Chip quality is inversely correlated with tuber sugar content. A total of 36 loci on 11 potato chromosomes were evaluated for natural DNA variation in 243 individuals. These loci included microsatellites and genes coding for enzymes that function in carbohydrate metabolism or transport (candidate loci). The markers were used to analyze population structure and were tested for association with the tuber quality traits. Highly significant and robust associations of markers with 1–4 traits were identified. Most frequent were associations with chip quality and tuber starch content. Alleles increasing tuber starch content improved chip quality and vice versa. With two exceptions, the most significant and robust associations (q<0.01) were observed with DNA variants in genes encoding enzymes that function in starch and sugar metabolism or transport. Comparing linkage and linkage disequilibrium between loci provided evidence for the existence of large haplotype blocks in the breeding materials analyzed.]]>
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DOI:10.1016/j.jbiotec.2015.01.019URLPMID:25661840 [本文引用: 1]
Potato tuber dormancy release is a critical development process that allows potato to produce new plant. The first Illumina RNA sequencing to generate the expressed mRNAs at dormancy tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) was performed. We identified 26,639 genes including 5,912 (3,450 up-regulated while 2,462 down-regulated) and 3,885 (2,141 up-regulated while 1,744 down-regulated) genes were differentially expressed from DT vs DRT and DRT vs ST. The RNA-Seq results were further verified using qRT-PCR. We found reserve mobilization events were activated before the bud emergence (DT vs DRT) and highlighted after dormancy release (DRT vs ST). Overexpressed genes related to metabolism of auxin, gibberellic acid, cytokinin and barssinosteriod were dominated in DT vs DRT, whereas overexpressed genes involved in metabolism of ethylene, jasmonate and salicylate were prominent in DRT vs ST. Various histone and cyclin isoforms associated genes involved in cell division/cycle were mainly up-regulated in DT vs DRT. Dormancy release process was also companied by stress response and redox regulation, those genes related to biotic stress, cell wall and second metabolism was preferentially overexpressed in DRT vs ST, which might accelerate dormancy breaking and sprout outgrowth. The metabolic processes activated during tuber dormancy release were also supported by plant seed models. These results represented the first comprehensive picture of a large number of genes involved in tuber dormancy release process.
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DOI:10.3389/fpls.2018.00315URLPMID:29593769 [本文引用: 8]
Cold-induced sweetening (CIS) caused by reducing sugar (RS) accumulation during storage in low temperature in potato tubers is a critical factor influencing the quality of fried potato products. The reconditioning (REC) by arising storage temperature is a common measure to lower down RS. However, both CIS and REC are genotype-dependent and the genetic basis remains uncertain. In the present study, with a diploid potato population with broad genetic background, four reproducible QTL of CIS and two of REC were resolved on chromosomes 5, 6, and 7 of the CIS-sensitive parent and chromosomes 5 and 11 of the CIS-resistant parent, respectively, implying that these two traits may be genetically independent. This hypothesis was also supported by the colocalization of two functional genes, a starch synthesis gene AGPS2 mapped in QTL CIS_E_07-1 and a starch hydrolysis gene GWD colocated with QTL REC_B_05-1. The cumulative effects of identified QTL were proved to contribute largely and stably to CIS and REC and confirmed with a natural population composed of a range of cultivars and breeding lines. The present research identified reproducible QTL for CIS and REC of potato in diverse conditions and elucidated for the first time their cumulative genetic effects, which provides theoretical bases and applicable means for tuber quality improvement.
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URLPMID:12011472 [本文引用: 1]
DOI:10.1073/pnas.0406674102URLPMID:15665090 [本文引用: 1]
The recently discovered potato tuber (Solanum tuberosum) alpha-glucan, water dikinase (GWD) (formerly known as R1) catalyzes the phosphorylation of starch by a dikinase-type reaction mechanism in which the beta-phosphate of ATP is transferred to either the C-6 or the C-3 position of the glucosyl residue of starch. In the present study, we found that the GWD enzyme is inactive in the oxidized form, which is accompanied by the formation of a specific intramolecular disulfide bond as determined by disulfide-linked peptide mapping. The regulatory properties of this disulfide linkage were confirmed by site-directed mutagenesis studies. Both reduced thioredoxin (Trx) f and Trx m from spinach leaves reduced and activated oxidized GWD at very low concentrations, with Trx f being the more efficient, yielding an S0.5 value of 0.4 microM. Interestingly, GWD displays a reversible and selective binding to starch granules depending on the illumination state of the plant. Here we show that starch granule-bound GWD isolated from dark-adapted plants exists in the inactive, oxidized form, which is capable of reactivation upon treatment with reduced Trx. Furthermore, the soluble form of GWD was found in its fully reduced state, providing evidence of a Trx-controlled regulation mechanism linking enzymatic activity and specific binding affinities of a protein to an intracellular surface. The regulatory site sequence, CFATC, of potato GWD is conserved in chloroplast-targeted GWDs from other species, suggesting an overall redox regulation of the GWD enzyme.
URLPMID:9592398 [本文引用: 1]
