多年生水稻分子图谱的构建与分析

doi:10.16288/j.yczz.24-340

遗传 ›› 2025, Vol. 47 ›› Issue (9): 1042-1056.doi: 10.16288/j.yczz.24-340

多年生水稻分子图谱的构建与分析

彭廷燊¹(), 陆久焱¹, 严雨欣¹, 谭霖¹, 南文斌¹, 秦小健¹, 李明¹, 龚俊义², 梁永书¹()

1.重庆师范大学，植物环境适应生物学重庆市重点实验室，重庆 401331
2.中国水稻研究所，杭州 310006

收稿日期:2024-12-03 修回日期:2025-01-11 出版日期:2025-04-08 发布日期:2025-04-08
通讯作者: 梁永书，博士，副教授：研究方向：多年生水稻种质资源创新利用。E-mail: Yongshuliang@yeah.net
作者简介:彭廷燊，硕士研究生，专业方向：多年生水稻种质资源。E-mail: pengtingshen@163.com
基金资助:
西南作物基因资源发掘与利用国家重点实验室“生物育种”揭榜挂帅重点项目(SKL-KF202226);重庆市自然科学基金面上项目(Cstc2021jcyj-msxmX0007);水稻生物育种国家重点实验室开放课题(20190202)

Construction and analysis of molecular genetic map of perennial Chinese rice

Tingshen Peng¹(), Jiuyan Lu¹, Yuxin Yan¹, Lin Tan¹, Wenbin Nan¹, Xiaojian Qin¹, Ming Li¹, Junyi Gong², Yongshu Liang¹()

1. Chongqing Key Laboratory of Plant Environmental Adaptation Biology, Chongqing Normal University, Chongqing 401331, China
2. National Rice Research Institute, Hangzhou 310006, China

Received:2024-12-03 Revised:2025-01-11 Published:2025-04-08 Online:2025-04-08
Supported by:
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China(SKL-KF202226);Natural Science Foundation of Chongqing City(Cstc2021jcyj-msxmX0007);Open Project Program of State Key Laboratory of Rice Biology(20190202)

摘要/Abstract

摘要：

培育多年生水稻新品种，实现“一种(年)多收”的节本增效种植模式是保障国家粮食安全最经济实惠的策略之一。本文对多年生水稻进行了分子图谱构建与分析，以期阐明多年生水稻微卫星位点的遗传规律。以2份多年生水稻构建2个半同胞(“黄糯2号/协青早B”和“长白7号/协青早B”) F₂群体为研究材料，绘制了两张分子图谱，分别包含108个和109个SSR标记，覆盖基因组全长2,036.10 cM和1,878.23 cM，标记间平均图距分别为18.85 cM和17.23 cM。卡方测验发现(P<0.05)，两群体基因型χ²值分别为134.85和291.02，极显著偏向父本“协青早B”。两图谱各连锁群基因型χ²值介于2.23~175.67和4.53~191.52，其中“黄糯2号”图谱第1、2、3、4、6、8、9、10和12连锁群基因型偏离孟德尔比，“长白7号”图谱第1、2、3、5、6、7、9、11和12连锁群基因型偏离孟德尔分离比。“黄糯2号”群体有38个单株基因型显著或极显著偏离孟德尔分离比，“长白7号”群体有47个单株基因型显著或极显著偏离孟德尔分离比。“黄糯2号”图谱有32个标记显著或极显著偏离孟德尔分离比，成簇分布在第3、4和6连锁群；“长白7号”有44个标记偏离孟德尔分离，成簇分布在第3、5、6、7、9和12连锁群。本研究为多年生水稻有利基因挖掘与种质资源创新利用奠定了基础。

关键词: 多年生水稻, SSR标记, 分子图谱, 基因型

Abstract:

To develop perennial rice varieties and realize one planting (year) more harvest planting pattern of increasing yield and farmer’s income is one of the most cost-effective strategy involved in safeguarding China’s grain supply. In this study, construction and analysis of molecular maps of perennial rice was performed to elucidate the genetic laws of microsatellite loci in perennial Chinese rice, two half-sib F₂ populations derived from two perennial Chinese japonica rice (HN2^#and CB7^#) crossed to the annual indica rice XieqingzaoB (XQZB) were developed to construct two half-sib linkage maps. We established linkage map lengths of 2,036.10 cM and 1,878.23 cM with average genetic distance of 18.85 cM and 17.23 cM by using 108 and 109 SSR markers in both HN2^# and CB7^# map, respectively. Chi-square value (χ²) for genotypes in the F₂populations of both HN2^# and CB7^# were 134.85 and 291.02, respectively, and exhibited extreme significant bias towards XQZB. χ² value for genotype on each linkage group of both HN2^#and CB7^# map ranged from 2.23 to 175.67, from 4.53 to 191.52, respectively. Genotypes on linkage groups of both the 1^st, 2^nd, 3^rd, 4^th, 6^th, 8^th, 9^th, 10^th, and 12^th in HN2^# map and 1^st, 2^nd, 3^rd, 5^th, 6^th, 7^th, 9^th, 11^th, and 12^th in CB7^# map deviated from the Mendelian ratio. There 38 F₂individual in HN2^# and 47 F₂ individual in CB7^#population deviated from the Mendelian ratio, respectively. Altogether 32 markers showed segregation distortion (29.63%) and clustered on the 3^rd, 4^th and 6^thof linkage in HN2^# map, there 44 markers showed segregation distortion (40.37%) and clustered on the 3^rd, 5^th, 6^th, 7^th, 9^th, and 12^th of linkage in CB7^# map. Overall, this study lays a good foundation for the mining of beneficial genes and the innovation and utilization of perennial Chinese rice genetic resources.

Key words: perennial Chinese rice, simple sequence repeat, molecular map, genotype

彭廷燊, 陆久焱, 严雨欣, 谭霖, 南文斌, 秦小健, 李明, 龚俊义, 梁永书. 多年生水稻分子图谱的构建与分析[J]. 遗传, 2025, 47(9): 1042-1056.

Tingshen Peng, Jiuyan Lu, Yuxin Yan, Lin Tan, Wenbin Nan, Xiaojian Qin, Ming Li, Junyi Gong, Yongshu Liang. Construction and analysis of molecular genetic map of perennial Chinese rice[J]. Hereditas(Beijing), 2025, 47(9): 1042-1056.

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染色体	标记数	“黄糯2号/协青早B”组合		“长白7号/协青早B”组合		公共多态性标记
染色体	标记数	多态性标记	多态性频率 (%)	多态性标记	多态性频率 (%)	多态性标记	多态性频率 (%)
1	57	13	22.81	14	24.56	8	14.04
2	47	9	19.15	9	19.15	5	10.64
3	67	17	25.37	14	20.90	9	13.43
4	41	9	21.95	8	19.51	7	17.07
5	47	9	19.15	9	19.15	6	12.77
6	56	9	16.07	13	23.21	7	12.50
7	36	12	33.33	13	36.11	9	25.00
8	29	11	37.93	9	31.03	9	31.03
9	30	5	16.67	5	16.67	5	16.67
10	36	6	16.67	7	19.44	4	11.11
11	35	3	8.57	2	5.71	0	0.00
12	26	5	19.23	6	23.08	5	19.23
总数	507	108	21.30	109	21.50	74	14.60

染色体	“黄糯2号/协青早B”F₂群体分子连锁图谱 (cM)			“长白7号/协青早B”F₂群体分子连锁图谱 (cM)
染色体	遗传距离	标记间平均图距	变幅	遗传距离	标记间平均图距	变幅
1	266.61	20.51	6.32~87.69	243.30	17.38	17.38 ~84.22
2	210.33	23.37	5.48~68.29	188.97	21.00	21.00~48.00
3	324.97	19.12	3.18~55.20	230.36	16.45	16.45~49.17
4	179.39	19.93	6.19~58.06	176.87	22.11	22.11~68.60
5	189.86	21.10	10.48~41.47	211.58	23.51	23.51~94.63
6	149.03	16.56	2.38~40.67	133.67	10.28	10.28~21.65
7	177.54	14.80	3.06~42.77	144.96	11.15	11.15~21.91
8	197.73	17.98	1.16~60.12	151.22	16.80	16.80~40.37
9	40.84	8.17	2.47~25.58	99.53	19.91	19.91~47.93
10	100.71	16.79	15.01~24.99	106.64	15.23	15.23~26.38
11	87.67	29.22	8.16~79.51	72.57	36.29	36.29~72.57
12	111.42	22.28	1.26~44.98	118.56	19.76	19.76~47.58
总计	2,036.10	18.85	5.43~52.44	1,878.23	17.23	17.23~51.92

	“黄糯2号/协青早B”F₂群体							“长白7号/协青早B”F₂群体
	基因型			总数	缺失	偏离方向	卡方值 (χ²)	基因型			总数	缺失	偏离方向	卡方值 (χ²)
	黄糯 2号	杂合	协青早B	总数	缺失	偏离方向	卡方值 (χ²)	长白 7号	杂合	协青早B	总数	缺失	偏离方向	卡方值 (χ²)
扩增条带数	1,844	4,497	2,621	8,962	542	协青早B	134.85>χ²_0.05= 5.99	1,744	4,116	2,822	8,682	910	协青早B	291.02>χ²_0.05= 5.99
百分比(%)	20.57	50.18	29.25	100	542	协青早B	134.85>χ²_0.05= 5.99	20.09	47.41	32.50	100	910	协青早B	291.02>χ²_0.05= 5.99

染色体	“黄糯2号/协青早B”F₂群体							“长白7号/协青早B”F₂群体
	多态性标记数	基因型			总数	卡方值 (χ²)	偏离方向	多态性标记数	基因型			总数	卡方值 (χ²)	偏离方向
	多态性标记数	黄糯2号	杂合	协青早B	总数	卡方值 (χ²)	偏离方向	多态性标记数	长白7号	杂合	协青早B	总数	卡方值 (χ²)	偏离方向
1	13	214	587	239	1,040	18.47^**	杂合	14	255	527	340	1,122	17.00^**	协青早B
2	9	141	359	231	731	22.39^**	协青早B	9	203	325	184	712	6.41^*	长白7号
3	17	237	609	562	1,408	175.67^**	协青早B	14	207	475	410	1,092	93.94^**	协青早B
4	9	132	381	226	739	24.63^**	协青早B	8	136	324	175	635	5.06	无
5	9	204	393	163	760	5.31	无	9	213	355	170	738	6.07^*	长白7号
6	9	123	362	263	748	53.18^**	协青早B	13	120	502	436	1,058	191.52^**	协青早B
7	12	262	519	233	1,014	2.23	无	13	179	547	366	1,092	64.05^**	协青早B
8	11	196	498	234	928	8.09^*	杂合	9	158	335	199	692	5.56	无
9	5	91	206	130	427	7.65^*	协青早B	5	79	180	144	403	25.56^**	协青早B
10	6	100	262	144	506	8.29^*	协青早B	7	105	267	130	502	4.53	无
11	3	62	106	72	240	4.10	无	2	24	43	72	139	53.36^**	协青早B
12	5	82	215	124	421	8.57^*	协青早B	6	65	236	196	497	70.32^**	协青早B

多年生水稻分子图谱的构建与分析

Construction and analysis of molecular genetic map of perennial Chinese rice

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Metrics

单株号	基因型			卡方值(χ²)	偏离方向	单株号	基因型			卡方值(χ²)	偏离方向
单株号	黄糯2号	杂合	协青早B	卡方值(χ²)	偏离方向	单株号	黄糯2号	杂合	协青早B	卡方值(χ²)	偏离方向
1	21	68	18	8.03^*	杂合	20	3	58	46	35.32^**	协青早B
2	23	67	14	10.21^**	杂合	21	21	44	42	11.62^**	协青早B
3	8	42	48	34.65^**	协青早B	22	17	66	21	7.85^*	杂合
4	16	42	32	6.09^*	协青早B	23	32	60	14	7.96^*	杂合
5	9	59	35	15.31^**	协青早B	24	9	54	39	18.00^**	协青早B
6	10	71	24	16.77^**	杂合	25	11	59	27	9.82^**	杂合
7	5	44	54	48.81^**	协青早B	26	26	33	40	14.96^**	协青早B
8	11	49	41	17.91^**	协青早B	27	14	49	34	8.26	协青早B
9	12	58	37	12.44^**	协青早B	28	20	40	43	15.41^**	协青早B
10	34	38	32	7.62^*	黄糯2号	29	16	65	24	7.17^*	杂合
11	9	66	29	15.23^**	杂合	30	23	44	37	6.23^*	协青早B
12	21	40	42	13.70^**	协青早B	31	15	60	30	6.43^*	杂合
13	21	63	17	6.50^*	杂合	32	14	56	31	6.92^*	协青早B
14	8	56	29	13.37^**	杂合	33	13	60	31	8.69^*	协青早B
15	16	50	38	9.46^**	协青早B	34	40	39	27	10.58^**	黄糯2号
16	12	48	47	24.03^**	协青早B	35	17	69	17	11.89^**	杂合
17	21	29	43	23.58^**	协青早B	36	20	25	36	18.19^**	协青早B
18	27	38	38	9.43^**	协青早B	37	24	40	41	11.46^**	协青早B
19	17	44	34	6.60	协青早B	38	15	37	35	11.14^**	协青早B

染色体	标记	基因型			卡方值 (χ²)	偏离方向	染色体	标记	基因型			卡方值 (χ²)	偏离方向
染色体	标记	黄糯2号	杂合	协早青B	卡方值 (χ²)	偏离方向	染色体	标记	黄糯2号	杂合	协早青B	卡方值 (χ²)	偏离方向
1	RM1297	12	48	14	6.65^*	杂合	4	RM401	11	54	21	7.95^*	杂合
1	RM8235	20	56	10	10.19^**	杂合	4	RM17303	12	46	29	6.93^*	杂合
2	RM5812	19	24	35	18.10^**	协青早B	4	RM2441	11	36	36	16.52^**	协青早B
2	RM1920	9	41	27	8.74^*	协青早B	4	RM17377	12	42	29	6.98^*	协青早B
2	RM1367	11	33	29	9.55^**	协青早B	4	RM348	11	50	25	6.84^*	杂合
3	RM14327	18	34	33	8.69^*	协青早B	5	RM1024	23	29	36	14.07^**	协青早B
3	RM6038	17	37	34	8.80^*	协青早B	5	RM6082	24	52	6	13.80^**	杂合
3	RM6849	16	30	29	7.51^*	协青早B	5	RM6229	29	50	0	26.87^**	黄糯2号
3	RM1002	5	37	43	35.40^**	协青早B	6	RM2615	13	38	35	12.42^**	协青早B
3	RM6417	5	31	39	33.08^**	协青早B	6	RM276	13	38	36	13.55^**	协青早B
3	RM7197	4	34	42	37.90^**	协青早B	6	RM7488	13	37	34	11.69^**	协青早B
3	RM4321	4	37	47	44.25^**	协青早B	6	RM564	0	53	23	25.76^**	杂合
3	RM232	4	38	36	26.31^**	协青早B	6	RM5957	11	43	28	7.24^*	协青早B
3	RM6080	1	42	41	38.10^**	协青早B	10	RM228	13	51	16	6.28^*	杂合
3	RM6959	9	21	48	55.62^**	协青早B	12	RM247	17	33	30	6.68^*	协青早B
3	RM3513	22	34	31	6.01^*	协青早B	12	RM7376	11	56	18	9.73^**	杂合

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