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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (12): 3045-3056.doi: 10.3724/SP.J.1006.2022.12080

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Development of functional markers and genotype screening for nitrogen use efficiency genes in rice

TAO Ya-Jun1,3(), ZHU Jing-Yan2, WANG Jun1,3, FAN Fang-Jun1,3, XU Yang1,3, LI Wen-Qi1,3, WANG Fang-Quan1,3, CHEN Zhi-Hui1,3, JIANG Yan-Jie1,3, ZHU Jian-Ping1,3, LI Xia1,3, YANG Jie1,3()   

  1. 1Jiangsu High Quality Rice Center / Nanjing Branch of Chinese National Center for Rice Improvement / Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, Jiangsu, China
    3Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Yangzhou University, Yangzhou 225009, Jiangsu, China
  • Received:2021-11-29 Accepted:2022-03-25 Online:2022-12-12 Published:2022-04-20
  • Contact: YANG Jie E-mail:ricetao@163.com;yangjie168@aliyun.com
  • Supported by:
    Jiangsu Province Key Research and Development Program Modern Agriculture(BE2020339);Natural Science Foundation of Jiangsu Province(BK20190255);National Natural Science Foundation of China(31901525);Jiangsu Province Key Research and Development Program Modern Agriculture(BE2021374);International Cooperation and Exchange of the National Natural Science Foundation of China(31861143011);Jiangsu Agricultural Science and Technology Innovation Fund(CX(19)1002)

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Abstract:

Nitrogen is an essential mineral element that affects plants biomass and yield formation, and its efficient and reasonable utilization is an important guarantee for sustainable agricultural. Breeding rice varieties containing high nitrogen use efficiency (NUE) genes is an effective way to increase NUE and reduce the amount of nitrogen fertilizer. In this study, five genes, OsNR2, OsNPF6.1, OsTCP19, OsLHT1, and OsGRF4, were selected from the aspects of nitrogen absorption, transportation, and assimilation. Based on the reported functional haplotype, co-segregated markers were designed. Using six pairs of allele-specific PCR (AS-PCR) markers and one pair of InDel marker, 70 indica rice, 34 japonica rice, and 84 Taihu rice resources were identified. The results showed that OsNR2 was widely distributed in indica rice, while OsNPF6.1, OsTCP19, and OsGRF4 were less distributed. All 34 japonica rice and 84 Taihu rice resources only contained OsLHT1. We also successfully obtained two indica germplasms, which contained OsNR2, OsNPF6.1, and OsGRF4. The functional markers developed in this research and two materials provide technical support for breeding new rice varieties with high NUE through molecular marker-assisted selection (MAS) methods.

Key words: rice, high nitrogen-use efficiency, AS-PCR, InDel markers

Table 1

Functional marker primers designed based mutation sites"

引物名称
Primer name		 引物序列
Primer sequence (5'-3')		 PCR片段大小
PCR fragment (bp)
NR2-F AGGGCGAGGACCCCAAGT
NR2-R GTCGTCGGGCTGGTCCCA 242
nr2-R GTCGTCGGGCTGGTCCCT 242
NPF6.1-F ATTATGGAACGGAGGGAG
NPF6.1-R CCCGGATGTCCACAACAC 246
npf6.1-R CCCGGATGTCCACAACAT 246
TCP19-INDEL-F TAACTCTTCAGGGTTCTTGC
TCP19-INDEL-R TGTGCCGTGTCACATAGA 253
LHT1-1-F GTTGCGGCTGACAATAAA
LHT1-1-R AGCATGGGGTCAAAGCAA 317
lht1-1-R AGCATGGGGTCAAAGCAG 317
LHT1-2-F TCATAATGCTTACCCTCT
LHT1-2-R TGGAGGGTTGACTCGTAA 166
lht1-2-R TGGAGGGTTGACTCGTAT 166
GRF4-1-F AACCAAATAAGCCCTTCA
GRF4-1-R ATGTGATAAAAAAGCTGTAA 329
grf4-1-R ATGTGATAAAAAAGCTGTAT 329
GRF4-2-F AACCAAATAAGCCCTTCA
GRF4-2-R TAGTTCACGCTAAAATTAG 410
grf4-2-R TAGTTCACGCTAAAATTAA 410

Fig. 1

Functional classification and variations of NUE genes in rice A: the functional classification of NUE genes; B: the variations of NUE genes."

Fig. 2

PCR amplification of different functional markers Lane 1, 3: NR2 marker; Lane 2, 4: nr2 marker; Lane 5, 7: NPF6.1 marker; Lane 6, 8: npf6.1 marker; Lane 9, 11: LHT1-1 marker; Lane 10, 12: lht1-1 marker; Lane 13, 15: LHT1-2 marker; Lane 14, 16: lht1-2 marker; Lane 17, 19: GRF4-1 marker; Lane 18, 20: grf4-1 marker; Lane 21, 23: GRF4-2 marker; Lane 22, 24: grf4-2 marker; Lane 25: PCR amplification of ‘Nipponbare’ using TCP19-INDEL marker; Lane 26: PCR amplification of ‘Kasalath’ using TCP19-InDel marker. M: DL2000 marker."

Table 2

Amplification parents and sites of designed functional markers"

标记名称
Marker name		 扩增亲本
Amplification parent		 扩增位点
Amplification site
NR2 NIP OsNR2779T
nr2 9311 OsNR2779A
NPF6.1 NIP OsNPF6.1160G
npf6.1 NJ11 OsNPF6.1160A
TCP19 NIP, Kasalath OsTCP启动子区29 bp的InDel A 29 bp InDel in the OsTCP19 promoter
LHT1-1 NIP OsLHT1-2140T
lht1-1 9311 OsLHT1-2140C
LHT1-2 NIP OsLHT1-595T
lht1-2 9311 OsLHT1-595A
GRF4-1 NIP OsGRF4-884T
grf4-1 RD23 OsGRF4-884A
GRF4-2 NIP OsGRF4-801C
grf4-2 RD23 OsGRF4-801T

Table 3

Distribution of NUE genes in indica"

材料Material OsNR2 OsNPF6.1 OsTCP19 OsLHT1-1 OsLHT1-2 OsGRF4-1 OsGRF4-2
951227 1 1 0 0 0 1 1
南京16 Nanjing 16 1 1 0 0 0 1 1
Z03108 1 1 0 0 0 0 0
04-286 1 1 0 0 0 0 0
扬稻8号 Yangdao 8 1 1 0 0 0 0 0
扬州98127 Yangzhou 98127 1 1 0 0 0 0 0
9311 1 1 0 0 0 0 0
中佳2号 Zhongjia 2 1 1 0 0 0 0 0
苏农3004 Sunong 3004 1 1 0 0 0 0 0
扬籼9850 Yangxian 9850 1 1 0 0 0 0 0
R6547 1 1 0 0 0 0 0
R6548 1 1 0 0 0 0 0
镇籼886 Zhenxian 886 1 0 0 0 0 0 0
IRRI超高产系 IRRI super high-yield line 1 0 0 0 0 0 0
金桂占选 Jinguizhanxuan 1 0 0 0 0 1 1
广超丝苗 Guangchaosimiao 1 0 0 0 0 0 0
玉香油占 Yuxiangyouzhan 1 0 0 0 0 0 0
银花占2号 Yinhuazhan 2 1 0 0 0 0 0 0
丰华占 Fenghuazhan 1 0 0 0 0 0 0
茉莉软占 Moliruanzhan 1 0 0 0 0 0 0
黄华占 Huanghuazhan 1 0 0 0 0 0 0
五山油占 Wushanyouzhan 1 0 1 0 0 0 0
茉莉丝占 Molisizhan 1 0 0 0 0 0 0
矮秀占 Aixiuzhan 1 0 0 0 0 0 0
茉莉油占 Moliyouzhan 1 0 0 0 0 0 0
丰新占 Fengxinzhan 1 0 1 0 0 0 0
黄美占 Huangmeizhan 1 0 0 0 0 0 0
黄莉占 Huanglizhan 1 0 0 0 0 0 0
黄丝占 Huangsizhan 1 0 0 0 0 0 0
丰二占 Feng’erzhan 1 0 0 0 0 0 0
华新占 Huaxinzhan 1 0 0 0 0 0 0
新514 Xin 514 1 1 0 0 0 0 0
R9912 1 0 0 0 0 1 1
浙恢7954 Zhehui 7954 1 0 0 0 0 0 0
泸恢17 Luhui 17 1 1 0 0 0 0 0
蜀恢881 Shuhui 881 1 0 0 0 0 0 0
恢76 Hui76 1 0 0 0 0 0 0
辐恢718 Fuhui 718 1 0 0 0 0 0 0
内香恢1号 Neixianghui 1 1 1 0 0 0 0 0
内多恢1号 Neiduohui 1 1 1 0 0 0 0 0
盐恢559 Yanhui 559 1 0 0 0 0 0 0
川恢725 Chuanhui 725 1 0 0 0 0 0 0
广恢128 Guanghui 128 1 0 0 0 0 0 0
湘747 Xiang 747 1 0 0 0 0 0 0
丰籼1号 Fengxian 1 1 0 0 0 0 0 0
小农占 Xiaonongzhan 1 0 0 0 0 0 0
五山丝苗 Wushansimiao 1 0 0 0 0 0 0
黄花占 Huanghuazhan 1 0 0 0 0 0 0
粤香占 Yuexiangzhan 1 0 0 0 0 0 0
粤禾丝苗 Yuehesimiao 1 1 0 0 0 0 0
粤综占 Yuezongzhan 1 1 0 0 0 0 0
粤农丝苗 Yuenongsimiao 1 1 0 0 0 0 0
金农丝苗 Jinnongsimiao 1 0 0 0 0 0 0
宁317 Ning 317 1 0 0 0 0 0 0
南农3017 Nannong 3017 1 1 0 0 0 0 0
泸恢195 Luhui 195 1 0 0 0 0 0 0
泸恢17 Luhui 17 1 0 0 0 0 0 0
桂99 Gui 99 1 0 0 0 0 0 0
辐恢838 Fuhui 838 1 0 0 0 0 0 0
Basmati-1 1 0 0 0 0 0 0
成恢149 Chenghui 149 1 0 0 0 0 0 0
绵恢725 Mianhui 725 1 1 0 0 0 0 0
E32辐照选-15 E32 radiation-15 1 1 0 0 0 0 0
成恢22 Chenghui 22 1 1 0 0 0 0 0
中香11 Zhongxiang 11 1 0 0 0 0 1 1
L30012 1 1 0 0 0 0 0
新513 Xin 513 1 0 0 0 0 0 0
胜泰1号 Shengtai 1 1 0 0 0 0 0 0
L30015 1 0 0 0 0 0 0
Kasalath 1 1 0 0 0 0 0

Table 4

Distribution of NUE genes in japonica"

材料Material OsNR2 OsNPF6.1 OsTCP19 OsLHT1-1 OsLHT1-2 OsGRF4-1 OsGRF4-2
连粳7号 Lianjing 7 0 0 0 1 1 0 0
连粳10号 Lianjing 10 0 0 0 1 1 0 0
徐稻3号 Xudao 3 0 0 0 1 1 0 0
淮稻5号 Huaidao 5 0 0 0 0 0 0 0
盐稻8号 Yandao 8 0 0 0 0 0 0 0
扬育粳2号 Yangyujing 2 0 0 0 1 1 0 0
扬9709 Yang 9709 0 0 0 1 1 0 0
扬中稻1号 Yangzhongdao 1 0 0 0 1 1 0 0
武陵粳1号 Wulingjing 1 0 0 0 1 1 0 0
扬辐粳1号 Yangfujing 1 0 0 0 1 1 0 0
宁粳1号 Ningjing 1 0 0 0 1 1 0 0
南粳49 Nanjing 49 0 0 0 1 1 0 0
南粳46 Nanjing 46 0 0 0 1 1 0 0
南粳5055 Nanjing 5055 0 0 0 1 1 0 0
苏沪香粳 Suhuxiangjing 0 0 0 1 1 0 0
武香粳14号 Wuxiangjing 14 0 0 0 1 1 0 0
武运粳7号 Wuyunjing 7 0 0 0 1 1 0 0
武运粳23号 Wuyunjing 23 0 0 0 1 1 0 0
苏香粳2号 Suxiangjing 2 0 0 0 1 1 0 0
嘉33 Jia 33 0 0 0 1 1 0 0
嘉991 Jia 991 0 0 0 1 1 0 0
镇稻1号 Zhendao 1 0 0 0 1 1 0 0
日辉粳6号 Rihuijing 6 0 0 0 0 0 0 0
泗阳紫稻 Siyangzidao 0 0 0 1 1 0 0
楚粳39 Chujing 39 0 0 0 0 0 0 0
云光104 Yunguang 104 0 0 0 1 1 0 0
粳优165 Jingyou 165 0 0 0 1 1 0 0
小粒香 Xiaolixiang 0 0 0 1 1 0 0
越光BL Yueguang BL 0 0 0 1 1 0 0
苏秀867 Suxiu 867 0 0 0 1 1 0 0
苏垦118 Suken 118 0 0 0 0 0 0 0
东北194 Dongbei 194 0 0 0 1 1 0 0
临稻16 Lindao 16 0 0 0 1 1 0 0
降糖稻 Jiangtangdao 0 0 0 0 0 0 0

Table 5

Distribution of NUE genes in Taihu resources"

材料Material NR2 NPF6.1 TCP19 LHT1-1 LHT1-2 GRF4-1 GRF4-2
抱芯太湖青 Baoxintaihuqing 0 0 0 1 1 0 0
矮脚太湖青 Aijiaotaihuqing 0 0 0 1 1 0 0
上海青 Shanghaiqing 0 0 0 1 1 0 0
海冬青 Haidongqing 0 0 0 1 1 0 0
常梗青 Changenqing 0 0 0 1 1 0 0
立更青 Ligengqing 0 0 0 1 1 0 0
齐江青 Qijiangqing 0 0 0 1 1 0 0
矮种罗汉黄 Aizhongluohanhuang 0 0 0 1 1 0 0
呆长青 Daichangqing 0 0 0 1 1 0 0
万年青 Wannianqing 0 0 0 1 1 0 0
韭菜青 Jiucaiqing 0 0 0 1 1 0 0
茭白叶青 Jiaobaiyeqing 0 0 0 1 1 0 0
大红稻(老来红) Dahongdao 0 0 0 1 1 0 0
老头老来红 Laotoulaolaihong 0 0 0 1 1 0 0
早黑头红 Zaoheitouhong 0 0 0 1 1 0 0
晚罗汉稻 Wanluohandao 0 0 0 1 1 0 0
晚牛毛黄 Wanniumaohuang 0 0 0 1 1 0 0
TH93 0 0 0 1 1 0 0
白石稻 Baishidao 0 0 0 1 1 0 0
大量稻 Daliangdao 0 0 0 1 1 0 0
白薄稻 Baibodao 0 0 0 1 1 0 0
二黑稻 Eeheidao 0 0 0 1 1 0 0
摧稻 Cuidao 0 0 0 1 1 0 0
红虹稻 Hongxiadao 0 0 0 1 1 0 0
鹅营白粳稻 Eyingbaijingdao 0 0 0 1 1 0 0
大穗头粳稻 Dasuitoujingdao 0 0 0 1 1 0 0
矮子粳稻 Aizijingdao 0 0 0 1 1 0 0
长黄稻 Changhuangdao 0 0 0 1 1 0 0
矮黄稻 Aihuangdao 0 0 0 1 1 0 0
减晚慢种 Jianwanmanzhong 0 0 0 1 1 0 0
天下第一种 Tianxiadiyizhong 0 0 0 1 1 0 0
红芒种 Hongmangzhong 0 0 0 1 1 0 0
矮洁种 Aijiezhong 0 0 0 1 1 0 0
瓜田种 Guatianzhong 0 0 0 1 1 0 0
龙沟种 Longgouzhong 0 0 0 1 1 0 0
老大种 Laodazhong 0 0 0 1 1 0 0
老虎种 Laohuzhong 0 0 0 1 1 0 0
余山种 Yushanzhong 0 0 0 1 1 0 0
TH262 0 0 0 1 1 0 0
江北种 Jiangbeizhong 0 0 0 1 1 0 0
TH274 0 0 0 1 1 0 0
TH275 0 0 0 1 1 0 0
白稻头 Baidaotou 0 0 0 1 1 0 0
TH284 0 0 0 1 1 0 0
TH301 0 0 0 1 1 0 0
TH303 0 0 0 1 1 0 0
TH324 0 0 0 1 1 0 0
TH345 0 0 0 1 1 0 0
TH346 0 0 0 1 1 0 0
TH359 0 0 0 1 1 0 0
不留名 Buliuming 0 0 0 1 1 0 0
TH369 0 0 0 1 1 0 0
甩杀极 Shuaishaji 0 0 0 1 1 0 0
TH373 0 0 0 1 1 0 0
TH374 0 0 0 1 1 0 0
TH376 0 0 0 1 1 0 0
TH380 0 0 0 1 1 0 0
TH382 0 0 0 1 1 0 0
TH384 0 0 0 1 1 0 0
TH385 0 0 0 1 1 0 0
南束罗汉黄 Nanshuluohanhuang 0 0 0 1 1 0 0
润叶黄 Runyehuang 0 0 0 1 1 0 0
TH390 0 0 0 1 1 0 0
有芒旱稻 Youmanghandao 0 0 0 1 1 0 0
TH394 0 0 0 1 1 0 0
TH403 0 0 0 1 1 0 0
TH407 0 0 0 1 1 0 0
TH413 0 0 0 1 1 0 0
六十子粳 Liushizijing 0 0 0 1 1 0 0
东方红1号(穗1) Dongfanghong 1 0 0 0 1 1 0 0
小红早 Xiaohongzao 0 0 0 1 1 0 0
润叶黄 Runyehuang 0 0 0 1 1 0 0
早小白稻 Zaoxiaobaidao 0 0 0 1 1 0 0
抖山旱稻(陆稻) Doushanhandao 0 0 0 1 1 0 0
早飞来风 Zaofeilaifeng 0 0 0 1 1 0 0
一时兴 Yishixing 0 0 0 1 1 0 0
头等一时兴 Toudengyishixing 0 0 0 1 1 0 0
香粳糯稻 Xiangjingnuodao 0 0 0 1 1 0 0
TH433 0 0 0 1 1 0 0
TH434 0 0 0 1 1 0 0
TH436 0 0 0 1 1 0 0
红芒糯 Hongmangnuo 0 0 0 1 1 0 0
TH438 0 0 0 1 1 0 0
TH444 0 0 0 1 1 0 0

Table 6

Sequencing primers for NUE genes designed and SNP (InDel) analysis"

引物名称 Primer name 引物序列 Primer sequence (5'-3')
NR2-CX F: AGGGCGAGGACCCCAAGT; R: TGTCGAGGTCATAGCCCATCTT
NPF6.1-CX F: ATTATGGAACGGAGGGAG; R: GGAGATAGAGGGTGGTGAA
TCP19-CX F: TAACTCTTCAGGGTTCTTGC; R: TGTGCCGTGTCACATAGA
LHT1-1-CX F: GTTGCGGCTGACAATAAA; R: AATCTCGTGGGAAATCTG
LHT1-2-CX F: TCATAATGCTTACCCTCT; R: TTGTTTTGCTAACTCACA
GRF4-CX F: AACCAAATAAGCCCTTCA; R: TTAGTCTGCTGCTCCAAC

Fig. 3

Sequence alignment of functional domains for partial rice varieties A:the partial sequence of OsNR2 in the 9311; B: the partial sequence of OsNPF6.1 in R6547; C: the partial sequence of OsLHT1-1 in SK118; D: the partial sequence of OsLHT1-2 in Huaidao 5; E: the partial sequence of OsGRF4-1 in Jinguizhanxuan; F: the partial sequence of OsGRF4-2 in Nanjing 16; G: the partial sequence of OsTCP19 in Wushanyouzhan. Red box indicates different SNP or InDel."

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