甘蔗3个育种性状与SSR标记的关联分析及优异等位变异发掘

doi:10.3724/SP.J.1006.2023.34066

Abstract

Abstract:

Cane yield and sucrose content are the two main breeding objectives in sugarcane, and plant height, stem diameter, and brix are major constituent factors of cane yield and sucrose. Identification of associated molecular markers and exploring elite alleles with yield and sucrose traits could provide a theoretical basis and reference for marker assisted breeding of sugarcane. In this study, 62 sugarcane germplasm entries were used as the experimental materials. Three breeding traits, including plant height, stem diameter, and brix were investigated under four planting environments at maturity stage. ANOVA, genetic variation analysis and association analysis between the identified from related markers for further allele effect analysis. The result of ANOVA revealed that genotype, planting environment and their interaction had significant effect on plant height, stem diameter and brix in sugarcane. The broad-sense heritability of the three traits ranged from 0.68 to 0.76, indicating that they had stable genetic characteristics and their phenotype was mainly determined by its genotype. The frequency of these three traits showed typical quantitative traits with normal distribution characteristics. The coefficients of variation of the three traits ranged from 6.73% to 19.89%, suggesting a rich variation in phenotypes. A total of 204 alleles were found with a mean of 5.5135 per marker. The average gene diversity coefficient was 0.6779, and the average PIC value was 0.6252. The 89.19% of total markers were highly polymorphic with PIC>0.5. Population structure analysis revealed that the tested group could be divided into three subgroups. A total of 20 markers were detected associated with plant height, stem diameter, and brix traits based on MLM method, which explained 5.04%-27.98% of phenotypic variation. Seven of them detected in two or more planting environments were considered as elite markers, 8 alleles with positive effect were identified and considered as the elite alleles, and 10 typical materials were found carrying these elite alleles by allele effect analysis. These results provide a great significance for candidate gene mining of yield and sucrose content traits and parents selection of hybrid combinations in sugarcane breeding.

Key words: sugarcane, breeding traits, SSR, association analysis, elite allele, allele effect

TIAN Chun-Yan, BIAN Xin, LANG Rong-Bin, YU Hua-Xian, TAO Lian-An, AN Ru-Dong, DONG Li-Hua, ZHANG Yu, JING Yan-Fen. Association analysis of three breeding traits with SSR markers and exploration of elite alleles in sugarcane[J].Acta Agronomica Sinica, 2024, 50(2): 310-324.

Figures/Tables 10

Table S1

Tested materials used in this study"

编号 Number	材料名称 Materials name	类型 Type
1	云瑞15-468 Yunrui 15-468	创新种质Innovation germplasm
2	云瑞17-142 Yunrui 17-142	创新种质Innovation germplasm
3	云瑞15-358 Yunrui 15-358	创新种质Innovation germplasm
4	云瑞17-135 Yunrui 17-135	创新种质Innovation germplasm
5	云瑞05-292 Yunrui 05-292	品系/亲本Line/parent
6	云瑞05-770 Yunrui 05-770	品系/亲本Line/parent
7	云瑞14-179 Yunrui 14-179	创新种质Innovation germplasm
8	云瑞14-177 Yunrui 14-177	创新种质Innovation germplasm
9	云瑞14-199 Yunrui 14-199	创新种质Innovation germplasm
10	云瑞17-146 Yunrui 17-146	创新种质Innovation germplasm
11	云瑞15-78 Yunrui 15-78	创新种质Innovation germplasm
12	云瑞03-315 Yunrui 03-315	品系/亲本Line/parent
13	云瑞17-148 Yunrui 17-148	创新种质Innovation germplasm
14	云瑞08-254 Yunrui 08-254	品系/亲本Line/parent
15	云瑞15-55 Yunrui 15-55	创新种质Innovation germplasm
16	云瑞17-133 Yunrui 17-133	创新种质Innovation germplasm
17	云瑞17-124 Yunrui 17-124	创新种质Innovation germplasm
18	云瑞15-566 Yunrui 15-566	创新种质Innovation germplasm
19	云瑞11-256 Yunrui 11-256	创新种质Innovation germplasm
20	云瑞17-114 Yunrui 17-114	创新种质Innovation germplasm
21	云瑞17-149 Yunrui 17-149	创新种质Innovation germplasm
22	云瑞15-503 Yunrui 15-503	创新种质Innovation germplasm
23	云瑞17-111 Yunrui 17-111	创新种质Innovation germplasm
24	云瑞15-56 Yunrui 15-56	创新种质Innovation germplasm
25	云瑞16-3 Yunrui 16-3	创新种质Innovation germplasm
26	云瑞16-4 Yunrui 16-4	创新种质Innovation germplasm
27	云瑞16 Yunrui 16	创新种质Innovation germplasm
28	云瑞37 Yunrui 37	创新种质Innovation germplasm
29	云瑞46 Yunrui 46	创新种质Innovation germplasm
30	云瑞52 Yunrui 52	创新种质Innovation germplasm
31	云瑞90 Yunrui 90	创新种质Innovation germplasm
32	云瑞151 Yunrui 151	创新种质Innovation germplasm
33	云瑞154 Yunrui 154	创新种质Innovation germplasm
34	云瑞164 Yunrui 164	创新种质Innovation germplasm
35	云瑞215 Yunrui 215	创新种质Innovation germplasm
36	云瑞258 Yunrui 258	创新种质Innovation germplasm
37	云蔗05-51 Yunzhe 05-51	品种/亲本Variety/parent
38	云蔗08-1609 Yunzhe 08-1609	品种/亲本Variety/parent
39	新台糖22号 ROC22	品种/亲本Variety/parent
40	新台糖16号 ROC16	品种/亲本Variety/parent
41	新台糖10号 ROC10	品种/亲本Variety/parent
42	粤糖60号 Yuetang 60	品种/亲本Variety/parent
43	粤糖93-159 Yuetang 93-159	品种/亲本Variety/parent
44	粤糖86-368 Yuetang 86-368	品种/亲本Variety/parent
45	粤糖00-236 Yuetang 00-236	品种/亲本Variety/parent
46	桂糖11号 Guitang 11	品种/亲本Variety/parent
47	赣蔗8号 Ganzhe 8	品种/亲本Variety/parent
48	柳城05-136 Liucheng 05-136	品种/亲本Variety/parent
49	福农15号 Funong 15	品种/亲本Variety/parent
50	福农39号 Funong 39	品种/亲本Variety/parent
51	崖城58-47 Yacheng 58-47	亲本Parent
52	崖城97-47 Yacheng 97-47	亲本Parent
53	园林6号 Yuanlin 6	品种/亲本Variety/parent
54	POJ3016	品种/亲本Variety/parent
55	POJ213	品种/亲本Variety/parent
56	Co475	品种/亲本Variety/parent
57	Q171	品种/亲本Variety/parent
58	Q208	品种/亲本Variety/parent
59	CP94-1196	品种/亲本Variety/parent
60	PK88-188	品种/亲本Variety/parent
61	VMC97-41	品种/亲本Variety/parent
62	SP81-3250	品种/亲本Variety/parent

Table S1

Table 1

Table 2

Fig. 1

Table 3

Fig. 2

Table 4

Table 5

Table 6

Table 7

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性状 Trait	变异来源 Source of variation	自由度 DF	总方差 SS	均方 MS	P值 P-value	广义遗传力 Broad-sense heritability
株高 PH	基因型 Genotype	61	525,860.4	8620.7	<0.001	0.68
	环境 Environment	3	595,918.2	198,639.4	<0.001
	基因型×环境 Genotype×Environment	183	321,306.8	1755.8	<0.001
茎径SD	基因型 Genotype	61	38.695,76	0.634,36	<0.001	0.76
	环境 Environment	3	132.009,44	44.003,15	<0.001
	基因型×环境 Genotype×Environment	183	13.438,21	0.073,43	<0.001
锤度Brix	基因型 Genotype	61	1383.048	22.673	<0.001	0.72
	环境 Environment	3	386.028	128.676	<0.001
	基因型×环境 Genotype×Environment	183	1007.080	5.503	<0.001

性状 Trait	种植环境 Planting environment	平均值±标准差 Mean±SD	最大值 Maximum	最小值 Minimum	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
株高 PH (cm)	FP_ND	263.48±28.25	324.73	197.60	10.72	-0.29	-0.41
	FP_NM	264.40±28.63	330.44	205.00	10.83	0.10	-0.23
	BP_RW	217.03±43.18	337.83	140.42	19.89	0.43	0.24
	BP_DS	200.74±34.38	289.58	131.67	17.13	0.02	-0.51
茎径 SD (cm)	FP_ND	2.50±0.34	3.44	1.67	13.64	0.06	0.05
	FP_NM	2.39±0.28	3.28	1.00	11.91	-0.38	1.76
	BP_RW	1.58±0.23	2.00	0.89	14.89	-0.15	-0.65
	BP_DS	1.62±0.21	2.06	1.11	12.98	-0.23	-0.32
锤度 Brix (%)	FP_ND	18.38±2.11	20.97	12.27	12.11	-1.49	1.89
	FP_NM	18.95±1.27	22.21	15.56	6.73	0.05	0.13
	BP_RW	17.97±1.92	22.42	13.93	10.71	0.19	-0.20
	BP_DS	18.68±1.88	23.02	15.56	10.04	0.41	-0.55

标记名称 Marker name	等位基因数 Alleles number	主要等位基因频率 Major allele frequency	多态性信息含量 PIC	基因多样性 Gene diversity
SMC334BS	9	0.3952	0.6605	0.7072
SMC336BS	9	0.2984	0.8129	0.8318
mSSCIR74	4	0.5000	0.5144	0.5951
mSSCIR3	7	0.2500	0.7961	0.8210
mSSCIR43	7	0.3790	0.6860	0.7288
SMC703BS	5	0.4435	0.6457	0.6951
SMC31CUQ	8	0.3387	0.7499	0.7802
SMC22DUQ	4	0.4435	0.5888	0.6554
SCB174	7	0.3145	0.7217	0.7607
SCB190	4	0.4194	0.6440	0.6976
DBF/Arb1	5	0.4194	0.6198	0.6778
DBF/Arb2	3	0.4758	0.4758	0.5704
DBF/Arb3	4	0.4919	0.4099	0.5235
Aqua/Arb1	2	0.5081	0.3749	0.4999
Aqua/Arb3	3	0.4355	0.5586	0.6353
SMC851MS	5	0.4113	0.6032	0.6645
SMC119CG	5	0.3387	0.6738	0.7248
SMC18SA	5	0.4113	0.6727	0.7172
SMC486CG	5	0.4435	0.6100	0.6700
SMC24DUQ	5	0.3145	0.7004	0.7453
SMC278CS	9	0.2661	0.8165	0.8362
SMC1604SA	5	0.5242	0.4876	0.5725
SMC7CUQ	4	0.5000	0.5599	0.6281
SMC1751CL	4	0.4194	0.5776	0.6457
SMC569CS	5	0.5242	0.5942	0.6424
SMC597CS	9	0.2500	0.7860	0.8124
mSSCIR66	5	0.3629	0.7107	0.7500
SMC36BUQ	5	0.3306	0.6590	0.7133
mSSCIR36	5	0.4677	0.6118	0.6677
SMC1825	4	0.5565	0.5665	0.6158
mSSCIR56	6	0.2984	0.7667	0.7964
SMC219	6	0.3710	0.6650	0.7158
SMC1752	5	0.4677	0.5913	0.6539
mSSCIR52	9	0.2500	0.8319	0.8490
IISR17b	4	0.3871	0.6698	0.7196
IISR111	3	0.4919	0.5528	0.6250
IISR306	10	0.2742	0.7918	0.8149
平均值 Mean	5.5135	0.4151	0.6252	0.6779

性状 Traits	关联位点个数 No. of associated loci	同时在2个及以上环境下检测到的位点数 No. of associated loci under two or more environments	表型变异解释率范围 Range of R² (%)
株高Plant height	6	1	10.57-14.95
茎径Stem diameter	7	4	5.04-26.29
锤度Brix	7	2	16.90-27.98

性状 Traits	标记 SSR markers	大田种植-南多 FP_ND	大田种植-弄门 FP_NM	桶栽-正常浇水 BP_RW	桶栽-干旱胁迫 BP_DS
株高 PH	SCB190	-	-	14.95^**	10.57^*
茎径 SD	DBF/Arb1	15.18^*	20.69^*	16.37^*	-
	SMC486CG	14.72^**	26.29^**	-	13.47^**
	SMC1752	-	21.56^**	12.40^*	-
	IISR306	-	25.36^**	-	5.04^*
锤度 Brix	SMC851MS	16.90^*	24.15^*	-	-
锤度 Brix	SMC119CG	27.98^**	-	-	26.50^*

Association analysis of three breeding traits with SSR markers and exploration of elite alleles in sugarcane

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性状 Trait	位点_等位变异 Locus_allele	表型效应Phenotypic effect of allele
性状 Trait	位点_等位变异 Locus_allele	FP_ND	FP_NM	BP_RW	BP_DS
株高 PH (cm)	SCB190_247 bp	-	-	-4.16	-2.81
	SCB190_250 bp	-	-	-7.64	-7.50
	SCB190_253 bp	-	-	-4.03	-1.59
	SCB190_259 bp	-	-	-0.16	-3.66
	SCB190_263 bp	-	-	+0.10	+2.02
茎径 SD (cm)	DBF/Arb1_217 bp	+0.01	+0.02	+0.07	-
	DBF/Arb1_221 bp	+0.01	-0.01	+0.03	-
	DBF/Arb1_222 bp	-0.01	-0.02	+0.02	-
	SMC486CG_222 bp	+0.06	+0.06	-	+0.06
	SMC486CG_232 bp	+0.02	+0.02	-	+0.01
	SMC486CG_234 bp	-0.01	-0.01	-	-0.01
	SMC486CG_236 bp	-0.07	-0.07	-	-0.06
	SMC486CG_237 bp	-0.03	-0.06	-	-0.04
	SMC486CG_238 bp	-0.18	-0.11	-	-0.09
	SMC486CG_242 bp	-0.09	+0.03	-	-0.02
	SMC1752_135 bp	-	+0.02	-0.02	-
	SMC1752_136 bp	-	-0.01	+0.01	-
	SMC1752_138 bp	-	+0.01	-0.01	-
	SMC1752_139 bp	-	-0.02	-0.03	-
	IISR306_133 bp	-	-0.16	-	-0.91
	IISR306_134 bp	-	-0.13	-	-0.92
	IISR306_138 bp	-	-0.01	-	-0.75
	IISR306_139 bp	-	+0.15	-	-0.75
	IISR306_141 bp	-	+0.04	-	-0.75
	IISR306_142 bp	-	+0.04	-	-0.75
	IISR306_143 bp	-	+1.04	-	-0.73
	IISR306_144 bp	-	+2.04	-	-0.73
锤度 Brix (%)	SMC851MS_129 bp	-0.11	-0.08	-	-
	SMC851MS_131 bp	-0.07	-0.09	-	-
	SMC851MS_132 bp	-0.16	+0.11	-	-
	SMC851MS_133 bp	+0.04	+0.01	-	-
	SMC851MS_134 bp	+0.22	+0.04	-	-
	SMC851MS_137 bp	-0.16	-0.26	-	-
	SMC119CG_110 bp	+0.44	-	-	-0.09
	SMC119CG_116 bp	+0.40	-	-	+0.20
	SMC119CG_122 bp	+0.01	-	-	+0.51
	SMC119CG_125 bp	-5.27	-	-	-0.68
	SMC119CG_132 bp	-0.31	-	-	+0.12

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