园艺学报 ›› 2023, Vol. 50 ›› Issue (5): 921-932.doi: 10.16420/j.issn.0513-353x.2022-0052
• 遗传育种·种质资源·分子生物学 • 下一篇
坎智勇, 张德辉(), 李中兴, 余思思, 钱谦, 樊天乐, 李雪薇, 马锋旺, 管清美()
收稿日期:
2022-11-01
修回日期:
2023-02-21
出版日期:
2023-05-25
发布日期:
2023-05-31
通讯作者:
*(E-mail:tsu.zhangdehui@163.com;)基金资助:
KAN Zhiyong, ZHANG Dehui(), LI Zhongxing, YU Sisi, QIAN Qian, FAN Tianle, LI Xuewei, MA Fengwang, GUAN Qingmei()
Received:
2022-11-01
Revised:
2023-02-21
Published:
2023-05-25
Online:
2023-05-31
摘要:
以90个苹果栽培品种为试验材料,采集冬季休眠的枝条进行相对电导率测定,评价其耐寒能力;同时利用基因组重测序技术检测到的1 247 162个SNP开展全基因组关联分析,筛选与苹果耐寒性状显著关联的候选基因。鉴定出3个耐寒能力最强的品种,其相对电导率均小于40%,分别是‘金红’(‘Jinhong’),‘埃德尔博斯多夫’(‘Edelborsdorfer’),‘赫拉森’(‘Haralson’)。基于1 247 162个高质量SNP位点与表征耐寒性的相对电导率的指标的关联分析,挖掘出5个与耐寒性显著关联的SNP位点,这些位点分布在4号、15号和16号染色体上,并鉴定到与冷胁迫紧密相关的3个候选基因TIF3B1(MD04G1241100)、COR47(MD15G1003900)和MD16G1069900。
中图分类号:
坎智勇, 张德辉, 李中兴, 余思思, 钱谦, 樊天乐, 李雪薇, 马锋旺, 管清美. 90个苹果品种耐寒性评价和全基因组关联分析[J]. 园艺学报, 2023, 50(5): 921-932.
KAN Zhiyong, ZHANG Dehui, LI Zhongxing, YU Sisi, QIAN Qian, FAN Tianle, LI Xuewei, MA Fengwang, GUAN Qingmei. Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis[J]. Acta Horticulturae Sinica, 2023, 50(5): 921-932.
名称 Name | 电导率/% Electrical conductivity | 名称 Name | 电导率/% Electrical conductivity | 名称 Name | 电导率/% Electrical conductivity |
---|---|---|---|---|---|
金红Jinhong | 34.43 ± 1.59 | 瑞丹Judaine | 48.29 ± 3.16 | A35 | 53.82 ± 3.23 |
埃德尔博斯多夫Edelborsdorfer | 38.98 ± 1.62 | Seromine | 48.39 ± 1.91 | 北海道9号Hokkaido 9 | 54.78 ± 2.54 |
赫拉森Haralson | 39.60 ± 2.26 | 瑞星Judestar | 48.50 ± 3.86 | 凯密欧Cameo | 55.00 ± 3.84 |
C32 | 41.19 ± 3.33 | 昂林Korin | 49.00 ± 1.30 | 荷斯坦Holstein | 55.52 ± 5.54 |
15 | 43.23 ± 3.43 | 王林Orin | 49.21 ± 3.19 | N1 | 55.52 ± 2.08 |
夕阳Sundowner | 43.40 ± 0.38 | Challenger | 49.27 ± 5.12 | 信浓红CinanoRed | 55.85 ± 3.76 |
蜜脆Honeycrisp | 43.41 ± 0.30 | 弘前富士Hirosakifuji | 49.36 ± 4.56 | Kiku | 55.85 ± 3.98 |
C10 | 43.85 ± 3.58 | 早红1号Early Red One | 49.42 ± 2.96 | 玫瑰光芒Rosy Glow | 55.98 ± 2.08 |
Ruby Mac | 43.97 ± 3.63 | 美味Ambrosia | 49.47 ± 0.49 | 皮诺娃Pinova | 56.18 ± 2.37 |
Halerstadter Jungfermapfe | 44.17 ± 2.98 | Northfield Beauty | 49.62 ± 3.39 | 凉香的季节Ryoka No Kisetsu | 56.29 ± 3.42 |
Redcord | 44.35 ± 1.60 | Juliana | 49.72 ± 3.99 | 皇家嘎拉Royal Gala | 56.35 ± 4.72 |
福拉瑞娜Florina | 44.37 ± 0.63 | 阿莱特Arlet | 49.91 ± 1.45 | AC | 56.36 ± 1.52 |
魔笛Modi | 44.57 ± 2.02 | N7 | 49.95 ± 3.25 | JA | 56.62 ± 1.34 |
红勋1号Hongxun 1 | 44.58 ± 3.21 | 秋光Qiuguang | 50.09 ± 0.78 | 千秋Senshu | 56.95 ± 1.21 |
Yellow Transparent | 44.69 ± 4.72 | 寒富Hanfu | 50.41 ± 3.95 | 富士2001 Fuji 2001 | 57.04 ± 2.81 |
Chenago Strawberry | 44.70 ± 2.34 | Reinders | 50.80 ± 3.23 | 鲁宾斯Rubens | 57.19 ± 1.50 |
甘红Ganhong | 45.15 ± 1.96 | 小国光Ralls | 51.03 ± 2.92 | 坎兹Kanzi | 57.26 ± 3.55 |
署红James Grieve | 45.58 ± 1.62 | 茜Akane | 51.09 ± 4.86 | Gloster69 | 57.31 ± 1.34 |
晨雾Morning Mist | 45.70 ± 1.69 | 秦阳Qinyang | 51.21 ± 2.62 | T22 | 57.33 ± 3.22 |
丽嘎啦 Regal Gala | 46.45 ± 3.55 | Goldgeld55544 | 51.26 ± 4.14 | Chanterler | 57.64 ± 1.10 |
1 | 46.50 ± 0.77 | Maririi Red | 51.27 ± 3.91 | Su | 58.38 ± 2.78 |
瑞林Jude-line | 46.78 ± 5.88 | NJ-90 | 51.92 ± 3.79 | 红盖露 Gale Gala | 59.12 ± 3.90 |
信浓甜Cinano Sweet | 47.30 ± 1.70 | K296 | 52.62 ± 3.88 | 平成Heisei | 59.43 ± 4.01 |
千秋Senshu | 47.39 ± 1.60 | Roho3615 | 53.04 ± 0.96 | 斯派克Spike | 60.03 ± 4.67 |
Pound Sweet | 47.98 ± 2.09 | Fujiko | 53.15 ± 2.80 | 粉金Pinkgold | 60.26 ± 0.91 |
威廉姆斯女士Lady Williams | 48.08 ± 1.90 | 秦冠Qinguan | 53.21 ± 1.95 | 太平洋玫瑰Pacific Rose | 60.81 ± 2.03 |
花嫁Wealthy | 48.17 ± 3.44 | 凉香Ryoka | 53.29 ± 4.36 | 红露Hongro | 61.00 ± 2.96 |
N9 | 48.19 ± 4.83 | 阿丽亚娜Ariane | 53.53 ± 1.21 | 大都Daitron | 63.03 ± 0.32 |
长富2号 Nagafu 2 | 48.22 ± 0.80 | Idared | 53.68 ± 3.42 | 布瑞本Braeburn | 64.61 ± 5.66 |
N2 | 48.25 ± 1.86 | C25 | 53.81 ± 2.59 | 津轻Tsugaru | 65.16 ± 5.71 |
表2 低温胁迫下苹果枝条的相对电导率
Table 2 The relative electrical conductivity of apple branches under low temperature stress
名称 Name | 电导率/% Electrical conductivity | 名称 Name | 电导率/% Electrical conductivity | 名称 Name | 电导率/% Electrical conductivity |
---|---|---|---|---|---|
金红Jinhong | 34.43 ± 1.59 | 瑞丹Judaine | 48.29 ± 3.16 | A35 | 53.82 ± 3.23 |
埃德尔博斯多夫Edelborsdorfer | 38.98 ± 1.62 | Seromine | 48.39 ± 1.91 | 北海道9号Hokkaido 9 | 54.78 ± 2.54 |
赫拉森Haralson | 39.60 ± 2.26 | 瑞星Judestar | 48.50 ± 3.86 | 凯密欧Cameo | 55.00 ± 3.84 |
C32 | 41.19 ± 3.33 | 昂林Korin | 49.00 ± 1.30 | 荷斯坦Holstein | 55.52 ± 5.54 |
15 | 43.23 ± 3.43 | 王林Orin | 49.21 ± 3.19 | N1 | 55.52 ± 2.08 |
夕阳Sundowner | 43.40 ± 0.38 | Challenger | 49.27 ± 5.12 | 信浓红CinanoRed | 55.85 ± 3.76 |
蜜脆Honeycrisp | 43.41 ± 0.30 | 弘前富士Hirosakifuji | 49.36 ± 4.56 | Kiku | 55.85 ± 3.98 |
C10 | 43.85 ± 3.58 | 早红1号Early Red One | 49.42 ± 2.96 | 玫瑰光芒Rosy Glow | 55.98 ± 2.08 |
Ruby Mac | 43.97 ± 3.63 | 美味Ambrosia | 49.47 ± 0.49 | 皮诺娃Pinova | 56.18 ± 2.37 |
Halerstadter Jungfermapfe | 44.17 ± 2.98 | Northfield Beauty | 49.62 ± 3.39 | 凉香的季节Ryoka No Kisetsu | 56.29 ± 3.42 |
Redcord | 44.35 ± 1.60 | Juliana | 49.72 ± 3.99 | 皇家嘎拉Royal Gala | 56.35 ± 4.72 |
福拉瑞娜Florina | 44.37 ± 0.63 | 阿莱特Arlet | 49.91 ± 1.45 | AC | 56.36 ± 1.52 |
魔笛Modi | 44.57 ± 2.02 | N7 | 49.95 ± 3.25 | JA | 56.62 ± 1.34 |
红勋1号Hongxun 1 | 44.58 ± 3.21 | 秋光Qiuguang | 50.09 ± 0.78 | 千秋Senshu | 56.95 ± 1.21 |
Yellow Transparent | 44.69 ± 4.72 | 寒富Hanfu | 50.41 ± 3.95 | 富士2001 Fuji 2001 | 57.04 ± 2.81 |
Chenago Strawberry | 44.70 ± 2.34 | Reinders | 50.80 ± 3.23 | 鲁宾斯Rubens | 57.19 ± 1.50 |
甘红Ganhong | 45.15 ± 1.96 | 小国光Ralls | 51.03 ± 2.92 | 坎兹Kanzi | 57.26 ± 3.55 |
署红James Grieve | 45.58 ± 1.62 | 茜Akane | 51.09 ± 4.86 | Gloster69 | 57.31 ± 1.34 |
晨雾Morning Mist | 45.70 ± 1.69 | 秦阳Qinyang | 51.21 ± 2.62 | T22 | 57.33 ± 3.22 |
丽嘎啦 Regal Gala | 46.45 ± 3.55 | Goldgeld55544 | 51.26 ± 4.14 | Chanterler | 57.64 ± 1.10 |
1 | 46.50 ± 0.77 | Maririi Red | 51.27 ± 3.91 | Su | 58.38 ± 2.78 |
瑞林Jude-line | 46.78 ± 5.88 | NJ-90 | 51.92 ± 3.79 | 红盖露 Gale Gala | 59.12 ± 3.90 |
信浓甜Cinano Sweet | 47.30 ± 1.70 | K296 | 52.62 ± 3.88 | 平成Heisei | 59.43 ± 4.01 |
千秋Senshu | 47.39 ± 1.60 | Roho3615 | 53.04 ± 0.96 | 斯派克Spike | 60.03 ± 4.67 |
Pound Sweet | 47.98 ± 2.09 | Fujiko | 53.15 ± 2.80 | 粉金Pinkgold | 60.26 ± 0.91 |
威廉姆斯女士Lady Williams | 48.08 ± 1.90 | 秦冠Qinguan | 53.21 ± 1.95 | 太平洋玫瑰Pacific Rose | 60.81 ± 2.03 |
花嫁Wealthy | 48.17 ± 3.44 | 凉香Ryoka | 53.29 ± 4.36 | 红露Hongro | 61.00 ± 2.96 |
N9 | 48.19 ± 4.83 | 阿丽亚娜Ariane | 53.53 ± 1.21 | 大都Daitron | 63.03 ± 0.32 |
长富2号 Nagafu 2 | 48.22 ± 0.80 | Idared | 53.68 ± 3.42 | 布瑞本Braeburn | 64.61 ± 5.66 |
N2 | 48.25 ± 1.86 | C25 | 53.81 ± 2.59 | 津轻Tsugaru | 65.16 ± 5.71 |
引物名称 Primer name | 正向引物(5′-3′) Forward primer | 反向引物(5′-3′) Reverse primer |
---|---|---|
MD04G1241100 | CAAAGAGAGGACTCATGGATACAAG | GTCCAGAAAGTGCGTTTGTAGAAC |
MD15G1003900 | AAGACTGAGGAGGTTCCAGTTGG | CTTCTCTTTCTCCTTGATGTCCTTG |
MD16G1069900 | GCTACATAGCATGAGGGACATGTTG | TCAAGCTCTGCCATGTTATCCAC |
表1 引物序列
Table 1 Primer sequence
引物名称 Primer name | 正向引物(5′-3′) Forward primer | 反向引物(5′-3′) Reverse primer |
---|---|---|
MD04G1241100 | CAAAGAGAGGACTCATGGATACAAG | GTCCAGAAAGTGCGTTTGTAGAAC |
MD15G1003900 | AAGACTGAGGAGGTTCCAGTTGG | CTTCTCTTTCTCCTTGATGTCCTTG |
MD16G1069900 | GCTACATAGCATGAGGGACATGTTG | TCAAGCTCTGCCATGTTATCCAC |
染色体 Chromosome | SNP位置/bp SNP position | 基因型 Genotype | SNP注释 SNP annotation | P值 P value |
---|---|---|---|---|
Chr04 | 31 829 140 | G/A | 外显子区域Exonic | 3.26E-06 |
31 821 706 | G/A | 内含子Intronic | 7.21E-06 | |
Chr15 | 238 509 | T/C | 外显子区域Exonic | 5.47E-06 |
7 277 652 | T/C | 外显子区域Exonic | 8.57E-06 | |
Chr16 | 4 918 081 | A/G | 基因间Intergenic | 4.22E-06 |
表3 苹果耐寒性显著相关的SNP
Table 3 SNPs significantly correlated with cold resistance
染色体 Chromosome | SNP位置/bp SNP position | 基因型 Genotype | SNP注释 SNP annotation | P值 P value |
---|---|---|---|---|
Chr04 | 31 829 140 | G/A | 外显子区域Exonic | 3.26E-06 |
31 821 706 | G/A | 内含子Intronic | 7.21E-06 | |
Chr15 | 238 509 | T/C | 外显子区域Exonic | 5.47E-06 |
7 277 652 | T/C | 外显子区域Exonic | 8.57E-06 | |
Chr16 | 4 918 081 | A/G | 基因间Intergenic | 4.22E-06 |
染色体 Chromosome | 物理位置/bp Position | 候选基因 Candidate gene | 基因注释或编码蛋白 Gene annotation or coding protein |
---|---|---|---|
Chr04 | 31 829 140 | MD04G1241100 | 翻译起始因子Translation inifiation factor TIF3B1 |
Chr15 | 238 509 | MD15G1003900 | 冷响应蛋白Cold-regulated protein COR47 |
Chr16 | 4 918 081 | MD16G1069900 | 编码叶绿体类囊体腔内的NAD(P)H脱氢酶复合物的1个亚基 A subunit of the NAD(P)H dehydrogenase complex located in the chloroplast thylakoid lumen |
表4 候选基因功能注释
Table 4 Functional annotations of candidate genes
染色体 Chromosome | 物理位置/bp Position | 候选基因 Candidate gene | 基因注释或编码蛋白 Gene annotation or coding protein |
---|---|---|---|
Chr04 | 31 829 140 | MD04G1241100 | 翻译起始因子Translation inifiation factor TIF3B1 |
Chr15 | 238 509 | MD15G1003900 | 冷响应蛋白Cold-regulated protein COR47 |
Chr16 | 4 918 081 | MD16G1069900 | 编码叶绿体类囊体腔内的NAD(P)H脱氢酶复合物的1个亚基 A subunit of the NAD(P)H dehydrogenase complex located in the chloroplast thylakoid lumen |
图4 COR47上SNP位点连锁不平衡分析(A)、显著SNP位点等位基因单体型分析(B)和Sanger测序验证(C)
Fig. 4 Linkage disequilibrium analysis of SNPs in COR47(A)allele haplotype analysis of significant SNP in COR47(B)and SNP was verified by Sanger sequencing(C)
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