马铃薯StDRO1基因的多态性鉴定及其与根系性状的关联分析

doi:10.3724/SP.J.1006.2022.04241

Abstract

Abstract:

In order to identify the single nucleotide polymorphism (SNP) of StDRO1 gene associated with potato root traits, StDRO1 gene coding region of the 110 tetraploid potato genotypes was cloned and sequenced. The association analysis between the StDRO1 SNPs and the major root traits of potato such as surface area, volume, and average diameter were carried out. The results showed that a SNP (G64C) was detected in the second exon of the StDRO1, 10 SNPs (G152A, A214G, A297G, C314T, A337T, T353C, T560A, C577A, C620A, and C625A) were identified in the third exon, and a SNP (T793A) was detected in the fourth exon. The association analysis indicated that in the total root volume, G152A locus of StDRO1 gene showed that GA genotype was superior to GG genotype (P < 0.05). In the average root diameter, C314 locus showed that CC genotype were superior to CT genotype (P < 0.05). In the root surface area, fresh weight, and dry weight, A337T locus showed that AT genotype were better than AA genotype (P < 0.05), while the locus in the average root diameter showed that AT genotype was significantly lower than AA genotype (P < 0.05). The root surface area, root volume, and fresh weight were showed as TC genotype > TT genotype (P < 0.05) in T353C site; the root volume was showed as CA genotype > CC genotype (P < 0.05) in C620A site; the root surface area, root volume, and fresh weight were showed as AT genotype > TT genotype (P < 0.05) in T793A site. In summary, the above six SNPs of StDRO1 genes had a significant impact on potato root traits, and the A337T, T353C, and T793A sites were particularly important. These results provide a basic theoretical reference for subsequent potato root architecture research and genetic improvement, but whether it could be used as a genetic marker for potato root traits need to be further verified by expanding the population sample.

Key words: potato, StDRO1 gene, root traits, association analysis, SNP

XU De-Rong, SUN Chao, BI Zhen-Zhen, QIN Tian-Yuan, WANG Yi-Hao, LI Cheng-Ju, FAN You-Fang, LIU Yin-Du, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of StDRO1 gene polymorphism and association analysis with root traits in potato[J].Acta Agronomica Sinica, 2022, 48(1): 76-85.

Figures/Tables 20

Table 1

Information of 110 potato materials"

材料编号 Material code	CIP号 CIP code	材料编号 Material code	CIP号 CIP code	材料编号 Material code	CIP号 CIP code
C2	CIP391065.69	C56	CIP394034.65	C99	CIP388615.22
C4	CIP392617.54	C57	CIP394034.7	C100	CIP389468.3
C5	CIP392634.52	C58	CIP394579.36	C101	CIP390637.1
C8	CIP393227.66	C59	CIP394600.52	C102	CIP391180.6
C9	CIP393228.67	C60	CIP394611.112	C103	CIP391533.1
C10	CIP393371.164	C61	CIP394613.139	C104	CIP391724.1
C11	CIP391004.18	C62	CIP394613.32	C105	CIP392032.2
C13	CIP393280.64	C63	CIP394614.117	C106	CIP392740.4
C14	CIP391047.34	C64	CIP394881.8	C107	CIP392745.7
C15	CIP391058.175	C65	CIP395186.6	C108	CIP392759.1
C16	CIP393085.5	C66	CIP395193.6	C109	CIP393613.2
C17	CIP398192.213	C67	CIP395195.7	C110	CIP393615.6
C18	CIP398098.119	C68	CIP395196.4	C112	CIP397030.31
C19	CIP398098.203	C70	CIP395432.51	C113	CIP397035.26
C20	CIP398180.253	C71	CIP395434.1	C114	CIP302428.20
C21	CIP398180.289	C72	CIP395436.8	C115	CIP302476.108
C23	CIP398180.612	C74	CIP396311.1	C116	CIP302499.30
C27	CIP398208.33	C79	CIP397029.21	C117	CIP304345.102
C28	CIP398208.58	C80	CIP397036.7	C119	CIP304350.118
C29	CIP398208.704	C81	CIP397039.51	C120	CIP304350.95
C30	CIP301024.14	C82	CIP397044.25	C121	CIP304371.67
C32	CIP301040.63	C83	CIP397055.2	C122	CIP304383.41
C33	CIP300046.22	C84	CIP397065.2	C123	CIP304383.80
C34	CIP300048.12	C85	CIP397067.2	C124	CIP304387.39
C35	CIP300054.29	C86	CIP397069.5	C127	CIP397077.16
C39	CIP300072.1	C87	CIP397073.15	C128	CIP391919.3
C41	CIP300099.22	C88	CIP397078.12	C130	CIP391931.1
C43	CIP379706.27	C89	CIP397079.26	C131	CIP394906.6
C44	CIP385499.11	C90	CIP397079.6	C132	CIP395438.1
C46	CIP388676.1	C91	CIP397098.12	C133	CIP394904.20
C48	CIP390478.9	C92	CIP397099.6	Atl	大西洋Atlantic
C49	CIP391207.2	C93	CIP397100.9	QS9	青薯9号Qingshu 9
C50	CIP391382.18	C94	CIP397196.3	GN2	甘农薯2号Gannongshu 2
C51	CIP392781.1	C95	CIP397196.8	LS3	陇薯3号Longshu 3
C52	CIP392797.22	C96	CIP397197.9	LS6	陇薯6号Longshu 6
C53	CIP392822.3	C97	CIP398014.2	Fa	费乌瑞它Favorita
C54	CIP392973.48	C98	CIP388611.22

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Table 4

Table 5

Table 6

Association analysis of StDRO1 gene polymorphism with root traits in potato"

单核苷酸多态性位点SNP	基因型Genotype	总根表面积 Surface area (cm²)	平均根系直径 Average diameter (mm)	总根体积 Root volume (cm³)	鲜重 Fresh weight (g)	干重 Dry weight (g)
G64C	GG	14.9413±3.1468 a	0.4150±0.0604 a	0.1412±0.0495 a	0.1393±0.0649 a	0.0107±0.0047 a
G64C	GC	14.0160±3.7477 a	0.4270±0.1101 a	0.1482±0.0577 a	0.1352±0.0568 a	0.0100±0.0053 a
G152A	GG	13.9844±3.5567 a	0.4237±0.1040 a	0.1415±0.0529 b	0.1335±0.0571 a	0.0102±0.0052 a
G152A	GA	15.7710±3.5351 a	0.4233±0.0660 a	0.1702±0.0629 a	0.1514±0.0672 a	0.0102±0.0048 a
A214G	AA	13.5207±3.4322 a	0.4401±0.1031 a	0.1509±0.0590 a	0.1283±0.0586 a	0.0094±0.0053 a
A214G	AG	14.7620±3.6443 a	0.4131±0.0948 a	0.1432±0.0531 a	0.1416±0.0590 a	0.0106±0.0049 a
A297G	AA	14.5685±3.2391 a	0.4056±0.0572 a	0.1340±0.0462 a	0.1400±0.0635 a	0.0107±0.0051 a
A297G	AG	14.1772±3.7271 a	0.4298±0.1087 a	0.1504±0.0578 a	0.1351±0.0576 a	0.0100±0.0051 a
C314T	CC	13.9384±3.4374 a	0.4378±0.1073 a	0.1475±0.0578 a	0.1302±0.0573 a	0.0096±0.0051 a
C314T	CT	15.0018±3.8743 a	0.3934±0.0683 b	0.1434±0.0503 a	0.1498±0.0609 a	0.0114±0.0050 a
A337T	AA	13.7373±3.4046 b	0.4372±0.1061 a	0.1465±0.0593 a	0.1282±0.0553 b	0.0094±0.0048 b
A337T	AT	15.4327±3.7782 a	0.3946±0.0731 b	0.1455±0.0466 a	0.1541±0.0633 a	0.0118±0.0053 a
单核苷酸多态性位点SNP	基因型Genotype	总根表面积 Surface area (cm²)	平均根系直径 Average diameter (mm)	总根体积 Root volume (cm³)	鲜重 Fresh weight (g)	干重 Dry weight (g)
T353C	TT	13.9052±3.5271 b	0.4238±0.1050 a	0.1407±0.0527 b	0.1312±0.0555 b	0.0100±0.0051 a
T353C	TC	15.9487±3.5253 a	0.4229±0.0639 a	0.1712±0.0613 a	0.1597±0.0691 a	0.0109±0.0052 a
T560A	AA	13.7829±3.3268 a	0.4295±0.1115 a	0.1381±0.0521 a	0.1303±0.0545 a	0.0100±0.0051 a
T560A	AT	15.0764±3.9096 a	0.4142±0.0732 a	0.1593±0.0585 a	0.1462±0.0649 a	0.0104±0.0051 a
C577A	CC	14.5161±3.7664 a	0.4038±0.0608 a	0.1363±0.0477 a	0.1432±0.0617 a	0.0109±0.0049 a
C577A	CA	14.1828±3.5511 a	0.4314±0.1092 a	0.1501±0.0579 a	0.1337±0.0580 a	0.0099±0.0052 a
C620A	CC	14.0477±3.6818 a	0.4018±0.0589 a	0.1307±0.0449 b	0.1407±0.0627 a	0.0103±0.0050 a
C620A	CA	14.4026±3.5725 a	0.4356±0.1132 a	0.1548±0.0589 a	0.1340±0.0570 a	0.0101±0.0052 a
C625A	CC	14.3825±3.5532 a	0.4159±0.0926 a	0.1450±0.0551 a	0.1334±0.0552 a	0.0099±0.0051 a
C625A	CA	14.0765±3.7234 a	0.4384±0.1087 a	0.1485±0.0565 a	0.1420±0.0658 a	0.0106±0.0052 a
T793A	TT	12.4573±2.7287 b	0.4114±0.0964 a	0.1259±0.0515 b	0.1134±0.0482 b	0.0086±0.0041 a
T793A	AT	14.7578±3.6593 a	0.4269±0.0994 a	0.1516±0.0554 a	0.1425±0.0602 a	0.0106±0.0053 a

Table 6

Table 6

Association analysis of StDRO1 gene polymorphism with root traits in potato"

单核苷酸多态性位点SNP	基因型Genotype	总根表面积 Surface area (cm²)	平均根系直径 Average diameter (mm)	总根体积 Root volume (cm³)	鲜重 Fresh weight (g)	干重 Dry weight (g)
G64C	GG	14.9413±3.1468 a	0.4150±0.0604 a	0.1412±0.0495 a	0.1393±0.0649 a	0.0107±0.0047 a
G64C	GC	14.0160±3.7477 a	0.4270±0.1101 a	0.1482±0.0577 a	0.1352±0.0568 a	0.0100±0.0053 a
G152A	GG	13.9844±3.5567 a	0.4237±0.1040 a	0.1415±0.0529 b	0.1335±0.0571 a	0.0102±0.0052 a
G152A	GA	15.7710±3.5351 a	0.4233±0.0660 a	0.1702±0.0629 a	0.1514±0.0672 a	0.0102±0.0048 a
A214G	AA	13.5207±3.4322 a	0.4401±0.1031 a	0.1509±0.0590 a	0.1283±0.0586 a	0.0094±0.0053 a
A214G	AG	14.7620±3.6443 a	0.4131±0.0948 a	0.1432±0.0531 a	0.1416±0.0590 a	0.0106±0.0049 a
A297G	AA	14.5685±3.2391 a	0.4056±0.0572 a	0.1340±0.0462 a	0.1400±0.0635 a	0.0107±0.0051 a
A297G	AG	14.1772±3.7271 a	0.4298±0.1087 a	0.1504±0.0578 a	0.1351±0.0576 a	0.0100±0.0051 a
C314T	CC	13.9384±3.4374 a	0.4378±0.1073 a	0.1475±0.0578 a	0.1302±0.0573 a	0.0096±0.0051 a
C314T	CT	15.0018±3.8743 a	0.3934±0.0683 b	0.1434±0.0503 a	0.1498±0.0609 a	0.0114±0.0050 a
A337T	AA	13.7373±3.4046 b	0.4372±0.1061 a	0.1465±0.0593 a	0.1282±0.0553 b	0.0094±0.0048 b
A337T	AT	15.4327±3.7782 a	0.3946±0.0731 b	0.1455±0.0466 a	0.1541±0.0633 a	0.0118±0.0053 a
单核苷酸多态性位点SNP	基因型Genotype	总根表面积 Surface area (cm²)	平均根系直径 Average diameter (mm)	总根体积 Root volume (cm³)	鲜重 Fresh weight (g)	干重 Dry weight (g)
T353C	TT	13.9052±3.5271 b	0.4238±0.1050 a	0.1407±0.0527 b	0.1312±0.0555 b	0.0100±0.0051 a
T353C	TC	15.9487±3.5253 a	0.4229±0.0639 a	0.1712±0.0613 a	0.1597±0.0691 a	0.0109±0.0052 a
T560A	AA	13.7829±3.3268 a	0.4295±0.1115 a	0.1381±0.0521 a	0.1303±0.0545 a	0.0100±0.0051 a
T560A	AT	15.0764±3.9096 a	0.4142±0.0732 a	0.1593±0.0585 a	0.1462±0.0649 a	0.0104±0.0051 a
C577A	CC	14.5161±3.7664 a	0.4038±0.0608 a	0.1363±0.0477 a	0.1432±0.0617 a	0.0109±0.0049 a
C577A	CA	14.1828±3.5511 a	0.4314±0.1092 a	0.1501±0.0579 a	0.1337±0.0580 a	0.0099±0.0052 a
C620A	CC	14.0477±3.6818 a	0.4018±0.0589 a	0.1307±0.0449 b	0.1407±0.0627 a	0.0103±0.0050 a
C620A	CA	14.4026±3.5725 a	0.4356±0.1132 a	0.1548±0.0589 a	0.1340±0.0570 a	0.0101±0.0052 a
C625A	CC	14.3825±3.5532 a	0.4159±0.0926 a	0.1450±0.0551 a	0.1334±0.0552 a	0.0099±0.0051 a
C625A	CA	14.0765±3.7234 a	0.4384±0.1087 a	0.1485±0.0565 a	0.1420±0.0658 a	0.0106±0.0052 a
T793A	TT	12.4573±2.7287 b	0.4114±0.0964 a	0.1259±0.0515 b	0.1134±0.0482 b	0.0086±0.0041 a
T793A	AT	14.7578±3.6593 a	0.4269±0.0994 a	0.1516±0.0554 a	0.1425±0.0602 a	0.0106±0.0053 a

Table 6

Table 7

Table 8

Table 9

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引物 Primer	引物序列 Primer sequences (5′-3′)	退火温度 Annealing temperature (℃)	产物片段长度 Product fragment length (bp)
DRO1-F	CCATTCAAACATCATCACAAGA	55	1670
DRO1-R	GAAATGGAACAACTAGCAGAGA	55	1670

单核苷酸多态性位点 SNP	样本数 Sample number	基因型频率 Genotype frequency		基因频率 Gene frequency		卡平方 χ²
G64C	110	GG 0.2818 (31)	GC 0.7182 (79)	G 0.6409	C 0.3591	34.5310
G152A	110	GG 0.8364 (92)	GA 0.1636 (18)	G 0.9182	A 0.0818	0.8734
A214G	110	AA 0.3909 (43)	AG 0.6091 (67)	A 0.6955	G 0.3045	21.0940
A297G	110	AA 0.2545 (28)	AG 0.7455 (82)	A 0.6273	G 0.3727	38.8385
C314T	110	CC 0.6818 (75)	CT 0.3182 (35)	C 0.8409	T 0.1591	3.9372
单核苷酸多态性位点 SNP	样本数 Sample number	基因型频率 Genotype frequency		基因频率 Gene frequency		卡平方 χ²
A337T	110	AA 0.6818 (75)	AT 0.3182 (35)	A 0.8409	T 0.1591	3.9372
T353C	110	TT 0.8182 (90)	TC 0.1818 (20)	T 0.9091	C 0.0909	1.1000
T560A	110	AA 0.6182 (68)	AT 0.3818 (42)	A 0.8091	T 0.1909	6.1242
C577A	110	CC 0.2818 (31)	CA 0.7182 (79)	C 0.6409	A 0.3591	34.5310
C620A	110	CC 0.3545 (39)	CA 0.6455 (71)	C 0.6773	A 0.3227	24.9768
C625A	110	CC 0.6545 (72)	CA 0.3455 (38)	C 0.8273	A 0.1727	4.7953
T793A	110	AT 0.7909 (87)	TT 0.2091 (23)	A 0.3955	T 0.6045	47.0682

单核苷酸多态性位点 SNP	样本数 Sample number	基因型频率 Genotype frequency		基因频率 Gene frequency		卡平方 χ²
G64C	110	GG 0.2818 (31)	GC 0.7182 (79)	G 0.6409	C 0.3591	34.5310
G152A	110	GG 0.8364 (92)	GA 0.1636 (18)	G 0.9182	A 0.0818	0.8734
A214G	110	AA 0.3909 (43)	AG 0.6091 (67)	A 0.6955	G 0.3045	21.0940
A297G	110	AA 0.2545 (28)	AG 0.7455 (82)	A 0.6273	G 0.3727	38.8385
C314T	110	CC 0.6818 (75)	CT 0.3182 (35)	C 0.8409	T 0.1591	3.9372
单核苷酸多态性位点 SNP	样本数 Sample number	基因型频率 Genotype frequency		基因频率 Gene frequency		卡平方 χ²
A337T	110	AA 0.6818 (75)	AT 0.3182 (35)	A 0.8409	T 0.1591	3.9372
T353C	110	TT 0.8182 (90)	TC 0.1818 (20)	T 0.9091	C 0.0909	1.1000
T560A	110	AA 0.6182 (68)	AT 0.3818 (42)	A 0.8091	T 0.1909	6.1242
C577A	110	CC 0.2818 (31)	CA 0.7182 (79)	C 0.6409	A 0.3591	34.5310
C620A	110	CC 0.3545 (39)	CA 0.6455 (71)	C 0.6773	A 0.3227	24.9768
C625A	110	CC 0.6545 (72)	CA 0.3455 (38)	C 0.8273	A 0.1727	4.7953
T793A	110	AT 0.7909 (87)	TT 0.2091 (23)	A 0.3955	T 0.6045	47.0682

单核苷酸多态性位点SNP	纯合度 Homozygosity	杂合度Heterozygosity	有效等位基因数 Effective number of alleles	多态信息含量 Polymorphism information content (PIC)
G64C	0.5397	0.4603	1.8528	0.3544
G152A	0.8498	0.1502	1.1768	0.1390
A214G	0.5764	0.4236	1.7349	0.3339
A297G	0.5324	0.4676	1.8783	0.3583
C314T	0.7324	0.2676	1.3653	0.2318
A337T	0.7324	0.2676	1.3653	0.2318
T353C	0.8347	0.1653	1.1980	0.1516
A560T	0.6911	0.3089	1.4470	0.2612
C577A	0.5397	0.4603	1.8528	0.3544
C620A	0.5629	0.4371	1.7767	0.3416
C625A	0.7142	0.2858	1.4001	0.2449
A793T	0.5219	0.4781	1.9162	0.3638

单核苷酸多态性位点SNP	纯合度 Homozygosity	杂合度Heterozygosity	有效等位基因数 Effective number of alleles	多态信息含量 Polymorphism information content (PIC)
G64C	0.5397	0.4603	1.8528	0.3544
G152A	0.8498	0.1502	1.1768	0.1390
A214G	0.5764	0.4236	1.7349	0.3339
A297G	0.5324	0.4676	1.8783	0.3583
C314T	0.7324	0.2676	1.3653	0.2318
A337T	0.7324	0.2676	1.3653	0.2318
T353C	0.8347	0.1653	1.1980	0.1516
A560T	0.6911	0.3089	1.4470	0.2612
C577A	0.5397	0.4603	1.8528	0.3544
C620A	0.5629	0.4371	1.7767	0.3416
C625A	0.7142	0.2858	1.4001	0.2449
A793T	0.5219	0.4781	1.9162	0.3638

Identification of StDRO1 gene polymorphism and association analysis with root traits in potato

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碱基类型 Base type	碱基位置Base site (bp)
碱基类型 Base type	64	152	214	297	314	337	353	560	577	620	625	793
参考基因组碱基类型 Base type of reference genome	G	G	A	A	C	A	T	T	C	C	C	T
变异碱基类型 Variant base type	C	A	G	G	T	T	C	A	A	A	A	A

基因型组合编号 Code of genotype combinations	基因型组合 Genotype combinations	总根表面积 Surface area (cm²)	鲜重 Fresh weight (g)
7-1	337AA+353TT+793AT	13.7148±3.3564 ab	0.1290±0.0530 ab
7-2	337AA+353TT+793TT	12.0009±2.2114 b	0.1028±0.0364 b
7-3	337AA+353TC+793AT	16.0900±3.6150 a	0.1532±0.0674 ab
7-4	337AA+353TC+793TT	14.7243±3.3069 ab	0.1583±0.0783 ab
7-5	337AT+353TT+793AT	15.3848±3.8763 ab	0.1515±0.0621 ab
7-6	337AT+353TT+793TT	11.6084±2.0201 b	0.1250±0.0230 ab
7-7	337AT+353TC+793AT	16.7491±3.0515 a	0.1808±0.0621 a

基因型组合编号 Code of genotype combinations	基因型组合 Genotype combinations	平均根系直径 Average diameter (mm)
8-1	314CC+337AA	0.4420±0.1073 a
8-2	314CC+337AT	0.3794±0.0992 a
8-3	314CT+337AA	0.3708±0.0600 a
8-4	314CT+337AT	0.3971±0.0698 a

基因型组合编号 Code of genotype combinations	基因型组合 Genotype combinations	总根体积 Root volume (cm³)
9-1	152GG+353TT+620CC+793AT	0.1399±0.0441 bc
9-2	152GG+353TT+620CC+793TT	0.0967±0.0229 c
9-3	152GG+353TT+620CA+793AT	0.1500±0.0558 bc
9-4	152GG+353TT+620CA+793TT	0.1344±0.0561 bc
9-5	152GG+353TC+620CA+793AT	0.1343±0.0098 bc
9-6	152GG+353TC+620CA+793TT	0.2247±0.0198 a
9-7	152GA+353TC+620CC+793AT	0.1347±0.0494 bc
9-8	152GA+353TC+620CC+793TT	0.1754±0.0511 ab
9-9	152GA+353TC+620CA+793AT	0.2186±0.0543 a
9-10	152GA+353TC+620CA+793TT	0.1053±0.0553 bc

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