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作物学报

作物学报 ›› 2024, Vol. 50 ›› Issue (1): 42-54.doi: 10.3724/SP.J.1006.2024.34047

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

烟草生物碱性状的QTL定位

刘颖超1(), 方敦煌2, 徐海明1, 童治军2,*(), 肖炳光2,*()   

  1. 1浙江大学农业与生物技术学院作物科学研究所, 浙江杭州 310058
    2云南省烟草农业科学研究院国家烟草基因工程研究中心, 云南昆明650021
  • 收稿日期:2023-03-09 接受日期:2023-06-29 出版日期:2024-01-12 网络出版日期:2023-07-19
  • 通讯作者: *童治军, E-mail: tzj861@163.com; 肖炳光, E-mail: xiaobgsubmission@126.com
  • 作者简介:E-mail: 22016031@zju.edu.cn
  • 基金资助:
    中国烟草总公司(110202101002);中国烟草总公司(110202101038(JY-15));云南省烟草公司项目(2021530000241013);云南省烟草公司项目(2022530000241009)

QTL mapping of alkaloids in tobacco

LIU Ying-Chao1(), FANG Dun-Huang2, XU Hai-Ming1, TONG Zhi-Jun2,*(), XIAO Bing-Guang2,*()   

  1. 1Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
    2National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, Yunnan, China
  • Received:2023-03-09 Accepted:2023-06-29 Published:2024-01-12 Published online:2023-07-19
  • Contact: *E-mail: tzj861@163.com; E-mail: xiaobgsubmission@126.com
  • Supported by:
    China National Tobacco Company(110202101002);China National Tobacco Company(110202101038(JY-15));Yunnan Tobacco Company(2021530000241013);Yunnan Tobacco Company(2022530000241009)

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摘要：

生物碱是烟草的重要化学成分。为明确烟草生物碱的遗传结构, 发掘控制相关性状的主效位点, 以烟草品种Y3、K326为亲本, 构建大小为271的重组自交系群体。分别于2018、2019和2020年在云南省昆明市石林、玉溪市研和种植群体材料, 检测总植物碱(TPA)、烟碱(NIC)、降烟碱(NOR)、假木贼碱(ANAB)和新烟草碱(ANAT) 5种生物碱表型。对群体进行基因组测序, 构建包含46,129个标记的遗传连锁图谱。利用基于混合线性模型的QTL定位方法及软件QTLNetwork 2.0, 进行QTL定位分析。共定位15个具有显著加性效应的QTL, 加性效应对表型贡献率为0.58%~11.57%。其中4个主效QTL即控制总植物碱的qTPA14、烟碱的qNIC14、假木贼碱的qANAB14和新烟草碱的qANAT14, 均可以解释相应性状10%以上的表型变异, 且均位于14号连锁群上。6个QTL具有显著的加性与环境互作效应, 对表型贡献率为0.80%~1.81%。5对QTL具有显著加性-加性上位性效应, 对表型的贡献率为0.15%~2.31%。2对QTL具有显著的上位性与环境互作效应, 对表型的贡献率为0.81%~1.16%。研究结果为进一步分离候选基因、解析遗传机理和促进烟草生物碱性状分子改良奠定了基础。

关键词: 烟草, 重组自交系, 生物碱, 复杂性状, 基因与环境互作

Abstract:

Alkaloids are important chemical components in tobacco. In order to understand the genetic architecture of alkaloids in tobacco and identify major effect loci controlling alkaloids related traits, QTL mapping on tobacco alkaloids was performed. A set of 271 recombinant inbred lines (RIL) were constructed with Y3 and K326 as the parents. The RIL population was planted in Yanhe, Yuxi, Yunnan province and Shilin, Kunming, Yunnan province in 2018, 2019, and 2020, respectively. Five alkaloid phenotypes including total plant alkali (TPA), nicotine (NIC), nornicotine (NOR), anabasine (ANAB), and anatabine (ANAT) were measured. A linkage map of 46,129 markers was constructed by genome sequencing of the population. QTL mapping was performed by the software QTLNetwork 2.0 which was developed based on the mixed linear model. A total of 15 QTLs with significant additive effects were identified. The contribution rate of additive effect to the corresponding phenotypes varied from 0.58% to 11.57%. Four major QTLs, qTPA14 for total plant alkali, qNIC14 for nicotine, qANAB14 for anabasine, and qANAT14 for anatabine, accounted for more than 10% of phenotypic variation of the corresponding traits, which were located in linkage group 14. Six QTLs with significant additive-by-environment interaction effects were detected, their additive-by-environment interaction effects explained the phenotypic variation of 0.80%-1.81%. Five pairs of QTLs with significant additive-by-additive epistasis effects were detected, accounting for phenotypic variation from 0.15% to 2.31%, while two pairs of QTLs were detected with significant epistasis-by-environment interaction effects, which explaining the proportion of phenotypic variation from 0.81% to 1.16%. The results pave a foundation for further isolation of candidate genes, the dissection of genetic mechanism, and the molecular improvement of tobacco alkaloid traits.

Key words: tobacco, the recombinant inbred line, alkaloids, complex traits, gene by environment interaction

表1

4种环境组合下生物碱性状的统计"

性状
Trait		 环境
Environment		 平均值
Mean		 标准差
SD		 最小值
Min.		 最大值
Max.		 偏度
Skewness		 峰度
Kurtosis		 变异系数
CV (%)		 遗传率
h2 (%)
总植物碱TPA (%) E1 2.91 0.88 1.09 5.62 0.24 -0.39 30.18 31.13
E2 1.96 0.51 0.95 3.53 0.62 0.36 26.23
E3 3.05 0.86 1.09 5.67 0.44 0.03 28.15
E4 2.75 0.68 1.29 4.80 0.30 -0.24 24.75
BLUP 2.67 0.32 1.99 3.50 0.30 -0.43 11.90
烟碱NIC (%) E1 2.66 0.88 0.77 5.26 0.21 -0.42 33.14 31.05
E2 1.80 0.50 0.52 3.45 0.46 0.36 27.71
E3 2.96 0.84 0.78 5.41 0.27 -0.10 28.50
E4 — — — — — — —
BLUP 2.47 0.31 1.76 3.27 0.23 -0.43 12.47
降烟碱NOR (μg g-1) E1 323.24 92.82 113.16 586.11 0.15 -0.52 28.72 24.04
E2 197.69 50.33 74.67 356.27 0.54 0.36 25.46
E3 390.08 92.74 137.16 673.68 -0.04 -0.10 23.78
E4 312.18 64.27 154.84 467.82 0.14 -0.36 20.59
BLUP 305.66 26.84 240.70 387.73 0.09 -0.14 8.78
假木贼碱ANAB (μg g-1) E1 184.86 55.88 71.62 378.56 0.21 -0.31 30.23 32.87
E2 131.14 33.32 66.45 248.40 0.56 0.35 25.41
E3 201.90 56.25 60.71 364.08 0.48 0.10 27.86
E4 185.95 46.73 95.35 307.93 0.24 -0.64 25.13
BLUP 175.91 21.59 128.49 233.97 0.29 -0.51 12.28
新烟草碱ANAT (μg g-1) E1 423.22 123.71 152.32 845.40 0.12 -0.24 29.23 33.09
E2 278.98 85.46 110.45 570.15 0.46 0.27 30.63
E3 438.77 123.22 160.60 896.84 0.68 0.98 28.08
E4 358.88 95.42 139.84 604.16 0.25 -0.60 26.59
BLUP 374.94 48.42 264.46 528.55 0.36 -0.06 12.92

图1

4种环境组合下生物碱性状的表型相关与遗传相关 a~d: 在2018年石林、2018年研和、2019年石林和2020年石林下的表型相关性; e: 遗传相关性; *、**和***分别代表0.05、0.01和0.001概率水平的显著性。缩写同表1。"

图2

连锁图谱的标记密度分布 较红的颜色表示较密集的标记区域, 每条黑线表示标记位置。"

表2

24个连锁群中2类标记的概况"

连锁群
Linkage group		 标记总数
Number of markers		 SNP数
Number of SNPs		 InDel数
Number of InDels		 Bin数
Number of bin markers		 遗传距离
Genetic distance (cM)		 平均遗传距离
Average genetic
distance (cM)		 最大间距
Maximum
interval (cM)
LG1 4992 4878 114 335 122.53 0.366 3.51
LG2 4654 4422 232 393 148.74 0.378 2.77
LG3 4150 3987 163 459 182.63 0.398 12.42
LG4 3119 2940 179 399 133.28 0.334 7.82
LG5 2939 2819 120 315 110.54 0.351 4.07
LG6 2865 2786 79 440 201.11 0.457 17.47
LG7 2839 2698 141 270 112.76 0.418 3.89
LG8 2177 2054 123 322 180.90 0.562 9.90
LG9 1969 1892 77 304 141.53 0.466 22.87
LG10 1915 1826 89 315 123.29 0.391 4.81
LG11 1833 1742 91 326 156.48 0.480 16.23
LG12 1513 1409 104 253 148.98 0.589 27.35
LG13 1509 1416 93 388 166.83 0.430 4.25
LG14 1496 1417 79 283 133.81 0.473 4.07
LG15 1262 1203 59 403 198.03 0.491 4.07
LG16 1235 1172 63 344 168.90 0.491 5.94
LG17 1054 993 61 184 111.99 0.609 10.09
LG18 877 828 49 288 150.04 0.521 4.44
LG19 873 829 44 195 101.54 0.521 4.81
LG20 862 812 50 253 141.20 0.558 14.41
LG21 802 755 47 270 164.38 0.609 7.24
LG22 620 587 33 244 153.23 0.628 5.00
LG23 290 275 15 203 191.41 0.943 9.33
LG24 284 272 12 106 55.75 0.526 5.18
总计Total 46,129 44,012 2117 7292 3499.88 0.480 27.35

表3

生物碱相关QTL的加性效应及其与环境互作效应"

性状
Trait		 位点
QTL		 连锁群
LG		 左侧标记
M-		 右侧标记
M+		 位置
Position
(cM)		 区间范围
Support interval (cM)		 加性效应
a		 加性与环境互作效应 贡献率
ae1 ae2 ae3 ae4 ha2(%) hae2(%)
总植物碱TPA (%) qTPA6 6 Nitab4.5_0026397_260_SNP Nitab4.5_0468967_662_SNP 38.3 34.0-40.7 0.1626*** 0.1265** 3.21 1.25
qTPA9-1 9 Nitab4.5_0171306_975_SNP Nitab4.5_0000110_495033_SNP 1.0 0.0-3.0 0.1212*** 2.28 0.00
qTPA14 14 Nitab4.5_0286260_185_SNP Nitab4.5_0007629_107938_SNP 112.5 110.0-114.6 -0.3037*** 10.97 0.00
烟碱NIC (%) qNIC6 6 Nitab4.5_0095945_611_SNP Nitab4.5_0000743_512482_SNP 36.1 32.9-39.7 0.1789*** 0.0924* -0.1017* - 3.70 0.89
qNIC14 14 Nitab4.5_0007629_107938_SNP Nitab4.5_0121404_652_SNP 113.6 111.0-115.6 -0.2933*** - 10.04 0.00
降烟碱NOR (μg g-1) qNOR6 6 Nitab4.5_0468967_662_SNP Nitab4.5_0384377_155_SNP 38.4 35.1-39.4 16.2771*** 12.8686** -10.7226* 11.6036** -13.9089* 2.38 1.26
qNOR7 7 Nitab4.5_0318723_531_SNP Nitab4.5_0008152_101211_SNP 72.0 70.3-73.0 -10.5465*** 1.92 0.00
qNOR11 11 Nitab4.5_0558151_555_SNP Nitab4.5_0484178_611_SNP 151.1 150.0-156.5 6.5518** 12.0254** 0.58 0.80
qNOR14 14 Nitab4.5_0092225_197_SNP Nitab4.5_0286260_185_SNP 111.0 108.9-113.6 -19.2023*** 3.28 0.00
假木贼碱ANAB (μg g-1) qANAB6 6 Nitab4.5_0026397_260_SNP Nitab4.5_0468967_662_SNP 37.3 35.1-39.4 12.7296*** 10.2749*** -6.1859* 4.80 1.64
qANAB9-1 9 Nitab4.5_0171306_975_SNP Nitab4.5_0000110_495033_SNP 1.0 0.0-2.5 8.7332*** 2.91 0.00
qANAB14 14 Nitab4.5_0286260_185_SNP Nitab4.5_0007629_107938_SNP 112.5 110.0-114.6 -20.1681*** 11.57 0.00
新烟草碱ANAT (μg g-1) qANAT6 6 Nitab4.5_0026397_260_SNP Nitab4.5_0468967_662_SNP 37.3 36.2-39.4 33.035*** 22.9189*** -21.5076* 6.49 1.81
qANAT9 9 Nitab4.5_0171306_975_SNP Nitab4.5_0000110_495033_SNP 0 0.0-1.5 17.95*** 1.85 0.00
qANAT14 14 Nitab4.5_0286260_185_SNP Nitab4.5_0007629_107938_SNP 111.5 110.0-114.6 -41.9745*** 10.77 0.00

表4

生物碱性状QTL的加性-加性上位性及其环境互作效应与遗传率"

性状
Trait		 位点i
QTLi		 位点i的两侧标记
Intervali		 位置
Positioni
(cM)		 区间范围
Rangei
(cM)		 位点j
QTLj		 位点j的两侧标记
Intervalj		 位置
Positionj
(cM)		 区间范围
Rangej
(cM)		 上位性效应
aa		 上位性与环境互作效应 贡献率
aae1 aae2 aae3 aae4 $\mathrm{h}_{\mathrm{asa}}^{2}$
(%)		 $\mathrm{h}_{\cos }^{2}$
(%)
总植物碱TPA (%) qTPA1 Nitab4.5_0001423_298079_SNP-Nitab4.5_0007238_116369_SNP 55.4 52.6-57.5 qTPA9-2 Nitab4.5_0652147_514_SNP-Nitab4.5_0000051_663607_SNP 128.2 127.1-129.5 -0.1093* 0.1711** 0.00 1.16
烟碱NIC (%) qNIC9 Nitab4.5_0104939_1831_SNP-Nitab4.5_0477966_676_SNP 137.4 134.8-139.5 qNIC12 Nitab4.5_0000615_20115_Indel-Nitab4.5_0108357_1594_SNP 103.4 101.0-104.4 -0.1455*** - 2.31 0.00
降烟碱NOR
(μg g-1)		 qNOR12-1 Nitab4.5_0389330_419_SNP-Nitab4.5_0002082_72841_SNP 89.4 87.7-90.4 qNOR21-1 Nitab4.5_0006357_88789_SNP-Nitab4.5_0006203_164411_SNP 75.8 73.6-76.8 -7.5006** 1.03 0.00
qNOR12-2 Nitab4.5_0047695_600_Indel-Nitab4.5_0013671_17800_Indel 98.6 95.3-99.6 qNOR21-2 Nitab4.5_0002795_109963_SNP-Nitab4.5_0051563_356_SNP 81.3 78.9-83.6 -5.2883* 0.15 0.00
假木贼碱ANAB
(μg g-1)		 qANAB9-2 Nitab4.5_0104939_1831_SNP-Nitab4.5_0477966_676_SNP 136.4 134.8-137.5 qANAB12 Nitab4.5_0002161_245575_SNP-Nitab4.5_0000615_20115_Indel 103.3 101.0-104.4 -7.7137*** 1.76 0.00
新烟草碱ANAT
(μg g-1)		 qANAT3 Nitab4.5_0020528_167_SNP-Nitab4.5_0001196_316885_SNP 17.2 16.0-18.4 qANAT7 Nitab4.5_0130803_641_SNP-Nitab4.5_0010558_34998_SNP 20.4 13.2-23.2 -8.8321** 12.2295** 0.51 0.81

表5

主效QTL的候选基因"

位点
QTL		 物理位置
Position (bp)		 候选基因ID
Gene ID		 起始位置
Start position (bp)		 终止位置
End position (bp)		 基因功能描述
Gene function
qTPA14
qANAB14
qANAT14		 chr8: 7243916-7447394 Nt08g00269 7307457 7315038 类似ADP-核糖基化因子GTP酶激活蛋白AGD8 Probable ADP-ribosylation factor GTPase-activating protein AGD8
Nt08g00270 7315990 7323983 类泛素羧基末端水解酶21 Ubiquitin carboxyl-terminal hydrolase 21-like
Nt08g00271 7331412 7334559 未鉴定蛋白LOC104211529 Uncharacterized protein LOC104211529
Nt08g00272 7335169 7337638 未鉴定蛋白LOC109242621亚型X2 Uncharacterized protein LOC109242621 isoform X2
Nt08g00273 7406451 7416964 类含有锚蛋白重复序列蛋白At5g02620 Ankyrin repeat-containing protein At5g02620-like
Nt08g00274 7430649 7431218 未鉴定蛋白LOC107790963 Uncharacterized protein LOC107790963
qNIC14 chr8: 6624235-7243916 Nt08g00249 6655849 6662737 类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
Nt08g00250 6664408 6681005 类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
Nt08g00251 6819300 6826090 类蛋白磷酸酶2C 29 Protein phosphatase 2C 29-like
Nt08g00252 6827921 6832618 类叶绿体蛋白ABCI7 Protein ABCI7, chloroplastic-like
Nt08g00253 6857681 6858055 未鉴定蛋白LOC104089357 Uncharacterized protein LOC104089357
Nt08g00254 6867626 6872883 类铝激活苹果酸转运蛋白12 Aluminum-activated malate transporter 12-like
Nt08g00255 6875043 6879809 MND1-相互作用蛋白1 MND1-interacting protein 1
Nt08g00256 6885824 6888724 类植物细胞内Ras组相关LRR蛋白5 Plant intracellular Ras-group-related LRR protein 5-like
Nt08g00257 6949292 6960262 类AP-2复合体亚基mu AP-2 complex subunit mu-like
Nt08g00258 6963535 6969302 部分类AT-hook基序核定位蛋白10 AT-hook motif nuclear-localized protein 10-like, partial
Nt08g00259 6971645 6972022 未鉴定蛋白LOC107812243 Uncharacterized protein LOC107812243
Nt08g00260 6978849 6981270 类AT-hook基序核定位蛋白23 AT-hook motif nuclear-localized protein 23-like
Nt08g00261 7068807 7069085 未鉴定蛋白LOC104241148 Uncharacterized protein LOC104241148
Nt08g00262 7077078 7083605 未鉴定蛋白LOC104246313 Uncharacterized protein LOC104246313
Nt08g00263 7089737 7091966 未鉴定蛋白LOC107821627 Uncharacterized protein LOC107821627
Nt08g00264 7124300 7125049 未鉴定蛋白LOC104246315 Uncharacterized protein LOC104246315
Nt08g00265 7128787 7129137 未鉴定蛋白LOC107817882 Uncharacterized protein LOC107817882
Nt08g00266 7133456 7135411 类转录因子MYC2 Transcription factor MYC2-like
Nt08g00267 7222657 7230856 未鉴定蛋白LOC109206945 Uncharacterized protein LOC109206945
Nt08g00268 7231266 7233911 未鉴定蛋白LOC109207164 Uncharacterized protein LOC109207164
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