甘蔗品种的AFLP和SSR标记鉴定及其应用

doi:10.3724/SP.J.1006.2018.00723

Abstract

Abstract:

Genetic diversity and fingerprint of varieties are crucial reference for breeding, cultivar right protection and new cultivar extension. We used nine pairs of AFLP markers and 15 pairs of SSR markers to scan 38 new sugarcane varieties (lines) from the national variety regional testings, obtaining abundant fingerprint data. Among the total 348 AFLP bands, 248 were polymorphic, with a polymorphism rate of 72.26 %. In addition, among the total 180 SSR bands, 176 were polymorphic, with a polymorphism rate of 97.78 %. The genetic similarity coefficients of these 38 new varieties (lines) were distributed from 0.668 to 0.847. We explored the distribution characteristics of genetic similarity coefficients using the boxplot, observing the genetic basis of five series (FN, MT, YZ, YG, and GT) of the 38 new sugarcane varieties (lines) was approximately similar. The clustering analysis manifested that these 38 new sugarcane varieties (lines) were divided into two groups at the genetic similarity coefficient of 0.732, with a subgroup including FN09-2201 and GT06-1492 that had high heterogeneity. Moreover, there was a small subgroup containing ROC22 at the genetic similarity coefficient of 0.770. Except for ROC22, the subgroup also contained FN 07-3206, FN 40, HZ 22, GT 09-12, and LC 07-150. ROC22 has wide adaptability, high yield, high sugar content and other excellent characteristics, other varieties (lines) in the same subgroup should be more likely to have these excellent characteristics and higher extention potential. Finally, through selection of 60 efficient amplification sites in the identification of SSR markers, we constructed the fingerprints of these 38 new sugarcane varieties (lines), which should play an important role in variety identification and variety protection. This study is expected to be directly applied to guide the genetic diversity assessment and molecular fingerprinting identification of sugarcane germplasm, and also to provide references for the extention and layout of these varieties or their utilization as hybrid parents.

Key words: sugarcane, molecular marker, germplasm identification, group division, variety extension

Zhou-Tao WANG, Qian YOU, Shi-Wu GAO, Chun-Feng WANG, Zhu LI, Jing-Jing MA, You-Xiong QUE, Li-Ping XU, Jun LUO. Identification of Sugarcane Varieties by AFLP and SSR Markers and Its Application[J].Acta Agronomica Sinica, 2018, 44(05): 723-736.

Figures/Tables 10

Supplementary table 1

Thirty-eight sugarcane varieties (lines) from three rounds of national variety regional testings"

编号 No.	品种(系) Variety (line)	亲本组合 Parent combination	选育单位 Breeding institution	参试轮次 Round	系列 Series
1	福农07-2020 Funong 07-2020	粤糖91-976 × LC 85-384 Yuetang 91-976 × LC 85-384	福建农林大学甘蔗综合研究所 SIFAFU	10	FN
2	福农07-3206 Funong 07-3206	90-1211 × 77-797	福建农林大学甘蔗综合研究所 SIFAFU	10	FN
3	福农40 Funong 40	福农93-3406 × 粤糖91-976 Funong 93-3406 × Yuetang 91-976	福建农林大学甘蔗综合研究所 SIFAFU	10	FN
4	福农09-2201 Funong 09-2201	ROC 22 × 桂糖00-122 ROC 22 × Guitang 00-122	福建农林大学甘蔗综合研究所 SIFAFU	11	FN
5	福农09-7111 Funong 09-7111	桂糖96-44 × ROC 11 Guitang 96-44 × ROC 11	福建农林大学甘蔗综合研究所 SIFAFU	11	FN
6	福农09-12206 Funong 09-12206	CP 65-357 × 崖城97-40 CP 65-357 × Yacheng 97-40	福建农林大学甘蔗综合研究所 SIFAFU	12	FN
7	福农11-2105 Funong 11-2105	川蔗89-103 × 云瑞05-770 Chuanzhe 89-103 × Yunrui 05-770	福建农林大学甘蔗综合研究所 SIFAFU	12	FN
8	福农09-4095 Funong 09-4095	粤糖93-159 × 云蔗91-790 Yuetang 93-159 × Yunzhe 91-790	福建农林大学甘蔗综合研究所 SIFAFU	12	FN
9	闽糖06-1405 Mintang 06-1405	闽糖92-649 × ROC 10 Mintang 92-649 × ROC 10	福建省农业科学院甘蔗研究所 SRIFAAS	11	MT
10	闽糖07-2005 Mintang 07-2005	崖城73-512 × ROC 22 Yacheng 73-512 × ROC 22	福建省农业科学院甘蔗研究所 SRIFAAS	12	MT
11	闽糖09-104 Mintang 09-104	桂糖90-420 × ROC 10 Guitang 90-420 × ROC 10	福建省农业科学院甘蔗研究所 SRIFAAS	12	MT
编号 No.	品种(系) Variety (line)	亲本组合 Parent combination	选育单位 Breeding institution	参试轮次 Round	系列 Series
12	闽糖02-205 Mintang 02-205	崖城90-3 × ROC 10 Yacheng 90-3 × ROC 10	福建省农业科学院甘蔗研究所 SRIFAAS	10	MT
13	云蔗08-2060 Yunzhe 08-2060	粤糖93-159 × Q 121 Yuetang 93-159 × Q 121	云南省农业科学院甘蔗研究所 SRIYAAS	10	YZ
14	云蔗08-1095 Yunzhe 08-1095	CP 84 -1198 × 科5 CP 84-1198 × Ke5	云南省农业科学院甘蔗研究所 SRIYAAS	11	YZ
15	云蔗09-1028 Yunzhe 09-1028	云瑞15-178 × 闽糖86-2121 Yunrui 15-178 × Mintang 86-2121	云南省农业科学院甘蔗研究所 SRIYAAS	12	YZ
16	云蔗09-1601 Yunzhe 09-1601	CP 94-1100 × 川糖89-103 CP 94-1100 × Chuantang 89-103	云南省农业科学院甘蔗研究所 SRIYAAS	12	YZ
17	云瑞09-315 Yunrui 09-315	CL 69-52 × 云瑞05-285 CL 69-52 × Yunrui 05-285	云南省农业科学院甘蔗研究所 SRIYAAS	12	YZ
18	云瑞07-1433 Yunrui 07-1433	云瑞99-155 × L 75-20 Yunrui 99-155 × L75-20	云南省农业科学院甘蔗研究所 SRIYAAS	10	YZ
19	云瑞10-187 Yunrui 10-187	ROC 20 × 云瑞05-282 ROC20 × Yunrui 05-282	云南省农业科学院甘蔗研究所 SRIYAAS	12	YZ
20	云瑞10-701 Yunrui 10-701	云瑞08-18 × 云瑞05-704 Yunrui 08-18 × Yunrui 05-704	云南省农业科学院甘蔗研究所 SRIYAAS	12	YZ
21	德蔗07-36 Dezhe 07-36	桂糖92-66 × CP 67-412 Guitang 92-66 × CP 67-412	云南德宏州甘蔗科学研究所 SRIDY	11	DZ
22	德蔗09-78 Dezhe 09-78	桂糖94-119 × ROC 10 Guitang 94-119 × ROC 10	云南德宏州甘蔗科学研究所 SRIDY	12	DZ
23	德蔗09-84 Dezhe 09-84	桂糖94-119 × ROC 10 Guitang 94-119 × ROC 10	云南德宏州甘蔗科学研究所 SRIDY	12	DZ
24	粤甘43 Yuegan 43	粤糖93-213 × 粤糖93-159 Yuetang 93-213 × Yuetang 93-159	广州甘蔗糖业研究所 GSIRI	10	YG
25	粤甘46 Yuegan 46	粤糖00-236 × 桂糖96-211 Yuetang 00-236 × Guitang 96-211	广州甘蔗糖业研究所 GSIRI	10	YG
26	粤甘47 Yuegan 47	粤农73-204 × ROC 22 Yuenong 73-204 × ROC 22	广州甘蔗糖业研究所 GSIRI	11	YG
27	粤甘48 Yuegan 48	HOCP 95-988 × 粤糖97-76 HOCP 95-988 × Yuetang 97-76	广州甘蔗糖业研究所 GSIRI	12	YG
28	粤甘50 Yuegan 50	粤糖96-86 × 粤糖99-66 Yuetang 96-86 × Yuetang 99-66	广州甘蔗糖业研究所 GSIRI	12	YG
29	海蔗22 Haizhe 22	粤糖93-159 × ROC 22 Yuetang 93-159 × ROC 22	广州甘蔗糖业研究所 GSIRI	11	YG
30	桂糖06-2081 Guitang 06-2081	桂糖00-122 × 崖城97-47 Guitang 00-122 × Yacheng 97-47	广西农业科学院甘蔗研究所 SRIGAAS	11	GT
31	桂糖08-1180 Guitang 08-1180	ROC 26 × ROC 22	广西农业科学院甘蔗研究所 SRIGAAS	11	GT
32	桂糖06-1492 Guitang 06-1492	CP 72-1210 × 湛蔗92-126 CP 72-1210 × Zhanzhe 92-126	广西农业科学院甘蔗研究所 SRIGAAS	12	GT
33	桂糖09-12 Guitang 09-12	ROC 24 × 粤农79-780 ROC 24 × Yuenong 79-780	广西农业科学院甘蔗研究所 SRIGAAS	12	GT
编号 No.	品种(系) Variety (line)	亲本组合 Parent combination	选育单位 Breeding institution	参试轮次 Round	系列 Series
34	柳城07-500 Liucheng 07-500	粤糖92-1287 × CP 72-1210 Yuetang 92-1287 × CP 72-1210	柳城县甘蔗研究中心 SRCLC	10	LC
35	柳城07-150 Liucheng 07-150	粤糖85-177 × ROC 22 Yuetang 85-177 × ROC 22	柳城县甘蔗研究中心 SRCLC	11	LC
36	柳城07-506 Liucheng 07-506	粤糖85-177 × ROC 22 Yuetang 85-177 × ROC 22	柳城县甘蔗研究中心 SRCLC	12	LC
37	赣蔗07-538 Ganzhe 07-538	ROC 10 × CP 57-614	江西省甘蔗研究所 SRIJP	10	GZ
38	ROC 22		台湾糖业研究所 SPRIT	参照	ROC

Supplementary table 1

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Fig. 3

Fig. 4

Fig. 5

Fig. 6

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组合 Combination	引物名 Primer name	序列 Sequence (5°-3°)	引物名 Primer name	序列 Sequence (5°-3°)
1	E-ACA	GACTGCGTACCAATTC ACA	M-CTG	GATGAGTCCTGAGTAA CTG
2	E-ACT	GACTGCGTACCAATTC ACT	M-CAA	GATGAGTCCTGAGTAA CAA
3	E-AAC	GACTGCGTACCAATTC AAC	M-CAC	GATGAGTCCTGAGTAA CAC
4	E-ACT	GACTGCGTACCAATTC ACT	M-CAG	GATGAGTCCTGAGTAA CAG
5	E-ACA	GACTGCGTACCAATTC ACA	M-CAC	GATGAGTCCTGAGTAA CTC
6	E-ACT	GACTGCGTACCAATTC ACT	M-CAC	GATGAGTCCTGAGTAA CAC
7	E-AAC	GACTGCGTACCAATTC AAC	M-CAG	GATGAGTCCTGAGTAA CAG
8	E-ACT	GACTGCGTACCAATTC ACT	M-CTC	GATGAGTCCTGAGTAA CTC
9	E-ACC	GACTGCGTACCAATTC ACC	M-CAG	GATGAGTCCTGAGTAA CAG

引物名 Primer name	重复单元 Repeating unit	引物序列(正/反) Primer sequence (Positive/Reverse) (5°-3°)	退火温度 T_m(°C)
SMC334BS	(TG)₃₆	CAATTCTGACCGTGCAAAGAT/CGATGAGCTTGATTGCGAATG	60
SMC336BS	(TG)₂₃(AG)₁₉	ATTCTAGTGCCAATCCATCTCA/CATGCCAACTTCCAAACAGAC	62
SMC286CS	(TG)₄₃	TCAAATGGGACCTTATTGGAG/TCCCTCGATCTCCGTTGTT	58
SMC569CS	(TG)₃₇	GCGATGGTTCCTATGCAACTT/TTCGTGGCTGAGATTCACACTA	62
SMC119CG	(TTG)₁₂	TTCATCTCTAGCCTACCCCAA/AGCAGCCATTTACCCAGGA	58
SMC31CUQ	(TC)₁₀(AC)₂₂	CATGCCAACTTCCAATACAGACT/AGTGCCAATCCATCTCAGAGA	62
mSSCIR43	(GT)₃(AT)₂(GT)₂₉	ATTCAACGATTTTCACGAG/AACCTAGCAATTTACAAGAG	52
SEP17	(CCT)₉	ACCCTGCTGGTCTCCTCC/ACGTTCGACGTCGTGTAGTG	60
SEP23	(AGA)₉	GTGTTCAGGCAGATGGTCCT/GTCGATGGCACCGATTTATT	60
SEP59	(CGG)₉	TTCCATTTACTCCTCCGTGC/CTCCCCCTCCTCGTACTTGT	60
SEP6	(GCA)₅(ACA)₁₃	CAGCCCATTAACCAAGCAAT/GAAGCAGCTGTTGCTCACTG	60
SEP70	(GCG)₈	AACTCACCCAACAAAGCGAC/AGACGAAGAGCTCGTGGATG	60
SEP8	(CT)₁₇	CTTGCTTCCCCTTTACTCCC/GAGGCGCCTTACTGTTCTTG	60
SEP84	(GGT)₉	AGAGACCGTAATGGTGACCG/ACCACCACCACCACCATACT	60
SEP89	(CGT)₁₀	AGCTCTGATTTTTGGGGGTT/GGAAGACAGTGGACGAGGTC	60

标记类别 Marker sort	引物名 Primer name	多态性位点数 Number of polymorphic loci	总扩增位点数 Total site number	多态比例 Polymorphic percentage (%)	引物多态信息含量 PIC
SSR标记 SSR marker (100-350 bp)	SEP6	9	9	100	0.964
	SPE8	13	14	92.86	0.959
	SEP17	10	10	100	0.961
	SEP23	22	22	100	0.979
	SEP59	10	11	90.91	0.920
	SEP70	8	8	100	0.895
	SEP84	5	5	100	0.695
	SEP89	12	12	100	0.896
	SMC334BS	10	12	83.33	0.927
	SMC336BS	12	12	100	0.967
	SMC286CS	20	20	100	0.961
	SMC569CS	9	9	100	0.779
	SMC119CG	13	13	100	0.961
	SMC31CUQ	11	11	100	0.967
	mSSCIR43	12	12	100	0.973
	总数/平均数Total/average	176	180	97.78
标记类别 Marker sort	引物名 Primer name	多态性位点数 Number of polymorphic loci	总扩增位点数 Total site number	多态比例 Polymorphic percentage (%)	引物多态信息含量 PIC
AFLP标记 AFLP marker (1-500 bp)	E-ACA/M-CTG	37	58	63.79	0.974
	E-ACT/M-CAA	24	42	57.14	0.968
	E-AAC/M-CAC	26	36	72.22	0.968
	E-ACT/M-CAG	24	32	75.00	0.971
	E-ACA/M-CAG	22	27	81.48	0.968
	E-ACT/M-CAC	19	25	76.00	0.972
	E-AAC/M-CAC	29	37	78.38	0.972
	E-ACT/M-CTC	36	51	70.59	0.974
	E-ACC/M-CAG	31	40	77.50	0.974
	总数/平均数Total/average	248	348	71.26	0.971

Identification of Sugarcane Varieties by AFLP and SSR Markers and Its Application

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