江苏粳稻育成品种氮响应相关性状位点分析

doi:10.16819/j.1001-7216.2024.231004

中国水稻科学 ›› 2024, Vol. 38 ›› Issue (5): 535-543.DOI: 10.16819/j.1001-7216.2024.231004

江苏粳稻育成品种氮响应相关性状位点分析

唐伟杰¹^,², 陈海元¹^,², 张所兵¹^,², 唐骏¹^,², 林静¹^,², 方先文¹^,², 张抒南⁴, 肖宁⁵, 吴云雨⁵, 李爱宏⁵, 张云辉¹^,²^,³^,^*()

¹江苏省农业生物学重点实验室/江苏省农业科学院种质资源与生物技术研究所, 南京 210014
²生物育种钟山实验室, 南京 210014
³江苏省粮食作物现代生产技术协同创新中心, 江苏扬州 225009
⁴南京农业大学作物遗传与种质创新利用全国重点实验室, 南京 210095
⁵江苏里下河地区农业科学研究所, 江苏扬州 225009

收稿日期:2023-10-09 修回日期:2023-11-14 出版日期:2024-09-10 发布日期:2024-09-10
通讯作者: *email: zyhrice@163.com
基金资助:
国家自然科学基金青年科学基金项目(32302672);江苏省自然科学基金青年基金项目(BK20210153);江苏省自然科学基金青年基金项目(BK20210388);江苏省自然科学基金青年基金项目(3140);江苏省种业创新揭榜挂帅项目(JBGS【2021】012);生物育种钟山实验室项目(BM2022008-03)

Analysis of Nitrogen-response Related Loci in japonica Rice Varieties from Jiangsu Province

TANG Weijie¹^,², CHEN Haiyuan¹^,², ZHANG Suobing¹^,², TANG Jun¹^,², LIN Jing¹^,², FANG Xianwen¹^,², ZHANG Shunan⁴, XIAO Ning⁵, WU Yunyu⁵, LI Aihong⁵, ZHANG Yunhui¹^,²^,³^,^*()

¹Jiangsu Provincial Key Laboratory of Agrobiology/Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
²Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
³Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
⁴National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
⁵Institute of Agricultural Sciences for Lixiahe Region in Jiangsu Province, Yangzhou 225009, China

Received:2023-10-09 Revised:2023-11-14 Online:2024-09-10 Published:2024-09-10
Contact: *email: zyhrice@163.com

摘要/Abstract

摘要：

【目的】江苏省是水稻氮肥施用量较高的区域，且水稻品种选育历史悠久，种质来源广泛；为了鉴定江苏水稻品种的氮响应相关性状以及氮响应相关基因，筛选氮高效品系，最终降低氮肥用量。【方法】利用76份不同地区、不同选育时间育成的江苏粳稻品种为试验材料，利用GATK4等软件获取群体变异信息，并用Admixture软件分析群体结构，以三个不同氮肥处理水平，调查成熟期氮响应相关性状并分析氮响应相关位点。【结果】筛选到了华粳5号和宁粳5号等氮钝感品种；利用关联分析，发现了已知或已报道的氮相关基因（OsAMT1.2，OsNRT2.4和Fd-GOGAT1等）邻近位点；进一步分析了位点的优异变异和携带优异位点的品种。【结论】鉴定了江苏育成粳稻品种的氮响应差异和携带的优异位点，可为选育不同氮响应品种提供参考。

关键词: 氮响应, 品种筛选, 优异位点

Abstract:

【Objective】In order to identify nitrogen-response related traits and genes, the study was carried out in Jiangsu Province, a region with a long history of rice breeding and a wide range of germplasm sources, screening nitrogen efficient lines, and finally reducing the amount of nitrogen fertilizer.【Method】We used 76 japonica rice varieties bred in 1983-2014 from different regions of Jiangsu Province as experimental materials. We investigated nitrogen-response related traits at the maturity stage at three nitrogen fertilizer levels, as well as the nitrogen-response related loci. The GATK4 and Admixture software were used for population variations calling and population structure analysis.【Result】 We selected nitrogen insensitive varieties such as Huajing 5 and Ningjing 5. By using association analysis, we identified neighboring loci of known or reported nitrogen related genes (OsAMT1.2, OsNRT2.4 and Fd-GOGAT1, etc.); Further analysis focused on the favorable variation of these loci and the varieties carrying advantageous loci. 【Conclusion】 This study identified the differences in nitrogen response and excellent loci carried by japonica rice varieties in Jiangsu Province. The findings provide both genetic materials and superior loci for breeding nitrogen responsive varieties.

Key words: nitrogen-response, variety selection, superior site

唐伟杰, 陈海元, 张所兵, 唐骏, 林静, 方先文, 张抒南, 肖宁, 吴云雨, 李爱宏, 张云辉. 江苏粳稻育成品种氮响应相关性状位点分析[J]. 中国水稻科学, 2024, 38(5): 535-543.

TANG Weijie, CHEN Haiyuan, ZHANG Suobing, TANG Jun, LIN Jing, FANG Xianwen, ZHANG Shunan, XIAO Ning, WU Yunyu, LI Aihong, ZHANG Yunhui. Analysis of Nitrogen-response Related Loci in japonica Rice Varieties from Jiangsu Province[J]. Chinese Journal OF Rice Science, 2024, 38(5): 535-543.

图/表 8

表1 供试品种审定年份、品种数和代表性品种

Table 1. Variety approval year, number of varieties, and representative varieties

审定年份 Approval year	品种数 Number of varieties	代表品种 Representative varieties
1983−1990	2	盐粳2号、武育粳2号 Yanjing 2, Wuyujing 2
1991−2000	11	武育粳3号、镇稻88、淮稻5号、泗稻11 Wuyujing 3, Zhendao 88, Huaidao 5, Sidao 11
2001−2010	45	徐稻3号、华粳5号、连粳4号、南粳46 Xudao 3, Huadao 5, Lianjing 4, Nanjing 46
2011−2014	18	宁粳5号、扬粳805、南粳49、连粳11 Ningjing 5, Yangjing 805, Nanjing 49, Lianjing 11

图1 76份江苏粳稻育成品种地域分布和不同氮肥处理下的株高和有效穗数统计 A: 76份品种在江苏的分布情况。B, C: 高、中和低氮处理下株高和有效穗数。n = 76。*P < 0.05; ns, P≥0.05(Duncan多重极差检验)。

Fig. 1. Geographical distribution of 76 japonica varieties from Jiangsu Province and plant height and effective panicle number under different nitrogen treatments A, Geographical distribution of 76 varieties in Jiangsu Province. B and C, Plant height and effective panicle number under high, medium, and zero nitrogen treatments. NH, High nitrogen; MN, Medium nitrogen; LN, Zero nitrogen; n = 76. * P < 0.05; ns, P≥0.05(Duncan’s multiple range test).

图2 江苏76份育成品种株高和有效穗数不同氮处理比值频数分布

Fig. 2. Frequency distribution of plant height ratio and effective panicle number ratios(EPNR) between nitrogen treatments

图3 江苏76份育成粳稻品种的群体结构分析 A: 76份育成品种SNP在12条染色体上的分布；B: Neighbor-joining群体进化树分析，每个分支代表一个品种；C: 群体结构分析，Admixture软件计算的每个水稻品种属于4个亚群的后验概率，每个竖条表示一个品种，每个竖条内的彩色部分表示加入不同聚类的隶属系数（Q）。

Fig. 3. Population structure analysis of 76 japonica rice varieties A, Distribution of SNPs in 76 varieties on 12 chromosomes; B, Neighbor-joining population evolutionary tree analysis. Each branch represents a variety; C, Population structure analysis. Posterior probabilities of a variety belonging to four subpopulations were calculated by Admixture software. Each accession is represented by a vertical bar. The colored subsections within each vertical bar indicate membership coefficient (Q) of the accession to different clusters.

图4 不同氮肥处理间的株高比和有效穗数比的关联分析 A~C:不同氮肥处理株高比关联分析（A: 低氮/高氮; B: 低氮/中氮; C: 中氮/高氮）；D~F:不同氮肥处理有效穗数比关联分析（D: 低氮/高氮; E: 低氮/中氮; F: 中氮/高氮）。

Fig. 4. Association analysis of plant height ratio and effective panicle number ratio between nitrogen fertilizer treatments A, B and C, Association analysis of plant height ratio under different nitrogen treatments(A, Zero nitrogen/High nitrogen; B, Zero nitrogen/Medium nitrogen; C, Medium nitrogen/High nitrogen); D, E and F, Association analysis of effective panicle number ratio under different nitrogen treatments(D, Zero nitrogen/High nitrogen; E, Zero nitrogen/Medium nitrogen; F, Medium nitrogen/High nitrogen).

图5 距离已知氮素利用相关基因相近显著位点变异分析 REF：与参考基因组一致位点；ALT：变异位点。差异采用单因素方差分析（ANOVA）计算。

Fig. 5. Analysis of significant loci adjacent to known nitrogen utilization related genes REF, Reference site; ALT, Mutation site. The differences were calculated using one-way analysis of variance (ANOVA).

表2 氮响应相关显著位点数量统计

Table 2. Statistics of the number of nitrogen-response loci

品种Variety	S6_6595563	S2_24640294	S8_7618813	S7_9740940	S1_20637066	S7_27706813	S12_293167	合计Total
镇稻11号 Zhendao 11	N	Y	Y	Y	Y	Y	Y	6
南粳44 Nanjing 44	N	Y	Y	Y	Y	Y	Y	6
华粳5号 Huajing 5	Y	Y	Y	Y	Y	N	Y	6
苏香粳2号 Suxiangjing 2	Y	Y	Y	Y	Y	Y	N	6
盐稻815 Yandao 815	N	Y	Y	N	Y	Y	Y	5
徐稻6号 Xudao 6	N	Y	N	Y	Y	Y	Y	5
镇稻16号 Zhendao 16	N	Y	Y	Y	Y	NA	Y	5
武运粳21 Wuyunjing 21	Y	Y	Y	Y	N	N	Y	5
武运粳24 Wuyunjing 24	N	Y	Y	N	Y	Y	Y	5
武育粳20 Wuyujing 20	N	Y	Y	N	Y	Y	Y	5

图6 不同品种优异位点数量和群体结构分析 Admixture软件计算的10个水稻品种属于4个亚群的后验概率，每个竖条内的部分表示加入不同聚类的隶属系数（Q）。

Fig. 6. Analysis of the number of superior site and population structure in different varieties Posterior probabilities of each variety belonging to 4 subpopulations calculated by Admixture. Each accession is represented by a vertical bar. The subsections within a column indicate membership coefficient (Q) of the accession to clusters. SXJ2, Suxiangjing 2; WYJ21, Wuyunjing 21; WYJ24, Wuyunjing 24.

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江苏粳稻育成品种氮响应相关性状位点分析

Analysis of Nitrogen-response Related Loci in japonica Rice Varieties from Jiangsu Province

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