Crops ›› 2024, Vol. 40 ›› Issue (1): 40-47.doi: 10.16035/j.issn.1001-7283.2024.01.006

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Analysis on Genetic Diversity and Population Structure for Japonica Rice Varieties in Liaoning Province

Liu Dan1(), Wang Jiayu2(), Feng Zhangli1, Feng Bo3, Chen Wenfu2   

  1. 1College of Biology and Agriculture of Zunyi Normal University, Zunyi 563006, Guizhou, China
    2Rice Research Institute of Shenyang Agricultural University / Key Laboratory of Northeast Rice Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Shenyang 110866, Liaoning, China
    3College of Resources and Environment of Zunyi Normal University, Zunyi 563006, Guizhou, China
  • Received:2022-08-15 Revised:2023-01-12 Online:2024-02-15 Published:2024-02-20
  • Contact: Wang Jiayu E-mail:danlius@163.com;wangjiayu@syau.edu.cn

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Abstract:

To clarify the genetic relationship of japonica rice in Liaoning province, genetic diversity and population structure of 58 japonica rice varieties from nine breeding units in Liaoning province were analyzed using 54 pairs of SSR molecular markers. The results showed that among the 54 SSR primers, a total of 48 primers were polymorphic, accounting for 88.89%. A total of 150 alleles were detected by 48 polymorphic primers, and the alleles (Na) per locus ranged from 2 to 6 with the mean value of 3.13. The gene diversity indices (H) varied from 0.03 to 0.78 with an average of 0.33. The polymorphism information content (PIC) was changed from 0.03 to 0.74 with the average of 0.29. Comparative analysis of varieties bred by different breeding units, the genetic diversity of rice varieties from Liaoning Institute of Saline-Alkali Land Utilization was highest, the average PIC and the H were 0.30 and 0.34, respectively, while the Tieling Academy of Agricultural Sciences was lowest, the average PIC and the average H were 0.11 and 0.14, respectively. NJ cluster showed that 58 varieties could be divided into three groups, the “Dangeng” rice bred by Dandong Academy of Agricultural Sciences and “Tiegeng” rice bred by Tieling Academy of Agricultural Sciences were grouped Ⅰ and Ⅲ, respectively. The genetic structure analysis was performed based on model, 58 rice varieties could be divided into two groups, 32 of which belonged to group A and 26 belonged to group B.

Key words: Liaoning province, Japonica rice, SSR, Genetic diversity, Population structure

Table 1

The materials and their origins"

编号
Number		 材料名称
Material name		 来源
Origin		 城市
City		 编号
Number		 材料名称
Material name		 来源
Origin		 城市
City
1 辽农9911 辽宁省农业科学院耕作栽培研究所 沈阳 30 辽星10 辽宁省水稻研究所 沈阳
2 辽农979 辽宁省农业科学院耕作栽培研究所 沈阳 31 辽201 辽宁省水稻研究所 沈阳
3 辽农968 辽宁省农业科学院耕作栽培研究所 沈阳 32 沈稻47 沈阳农业大学 沈阳
4 辽盐2 辽宁省盐碱地利用研究所 盘锦 33 沈稻18 沈阳农业大学 沈阳
5 辽盐241 辽宁省盐碱地利用研究所 盘锦 34 沈稻9 沈阳农业大学 沈阳
6 辽盐283 辽宁省盐碱地利用研究所 盘锦 35 沈稻3 沈阳农业大学 沈阳
7 辽盐16 辽宁省盐碱地利用研究所 盘锦 36 沈稻6 沈阳农业大学 沈阳
8 盐粳34 辽宁省盐碱地利用研究所 盘锦 37 沈稻7 沈阳农业大学 沈阳
9 盐粳68 辽宁省盐碱地利用研究所 盘锦 38 沈农6014 沈阳农业大学 沈阳
10 盐粳48 辽宁省盐碱地利用研究所 盘锦 39 沈农159 沈阳农业大学 沈阳
11 盐粳456 辽宁省盐碱地利用研究所 盘锦 40 沈农9903 沈阳农业大学 沈阳
12 盐丰47 辽宁省盐碱地利用研究所 盘锦 41 沈农9816 沈阳农业大学 沈阳
13 盐188 辽宁省盐碱地利用研究所 盘锦 42 沈农606 沈阳农业大学 沈阳
14 雨田7号 盘锦北方农业技术开发有限公司 盘锦 43 沈农016 沈阳农业大学 沈阳
15 辽粳28 辽宁省水稻研究所 沈阳 44 千重浪2 沈阳农业大学 沈阳
16 辽粳5 辽宁省水稻研究所 沈阳 45 千重浪1 沈阳农业大学 沈阳
17 辽粳294 辽宁省水稻研究所 沈阳 46 沈农129 沈阳农业大学 沈阳
18 辽粳534 辽宁省水稻研究所 沈阳 47 沈农265 沈阳农业大学 沈阳
19 辽粳101 辽宁省水稻研究所 沈阳 48 沈农9741 沈阳农业大学 沈阳
20 辽粳454 辽宁省水稻研究所 沈阳 49 营8433 大石桥市农业技术推广中心 营口
21 辽粳326 辽宁省水稻研究所 沈阳 50 铁粳4 铁岭市农业科学院 铁岭
22 辽粳371 辽宁省水稻研究所 沈阳 51 铁粳7 铁岭市农业科学院 铁岭
23 辽粳9 辽宁省水稻研究所 沈阳 52 铁粳9 铁岭市农业科学院 铁岭
24 辽粳287 辽宁省水稻研究所 沈阳 53 丹粳10 丹东农业科学院 丹东
25 辽星1 辽宁省水稻研究所 沈阳 54 丹粳11 丹东农业科学院 丹东
26 辽星5 辽宁省水稻研究所 沈阳 55 丹粳1 丹东农业科学院 丹东
27 辽星12 辽宁省水稻研究所 沈阳 56 丹粳3 丹东农业科学院 丹东
28 辽星13 辽宁省水稻研究所 沈阳 57 丹粳9 丹东农业科学院 丹东
29 辽星20 辽宁省水稻研究所 沈阳 58 港源8 东港市示范繁殖农场 丹东

Table 2

Genetic diversity analysis of part japonica rice varieties in Liaoning with polymorphic SSR markers"

位点Locus Maf Na H PIC 位点Locus Maf Na H PIC
RM495 0.97 2.00 0.07 0.06 RM455 0.97 2.00 0.07 0.06
RM1 0.75 3.00 0.39 0.33 RM408 0.98 2.00 0.03 0.03
RM283 0.52 3.00 0.54 0.44 RM152 0.93 3.00 0.13 0.13
RM259 0.86 3.00 0.25 0.23 RM25 0.90 3.00 0.19 0.18
RM312 0.93 2.00 0.13 0.12 RM44 0.40 5.00 0.67 0.61
RM5 0.40 4.00 0.69 0.62 RM223 0.69 4.00 0.49 0.46
RM246 0.47 5.00 0.67 0.62 RM284 0.91 3.00 0.16 0.15
RM237 0.95 2.00 0.10 0.09 RM447 0.53 3.00 0.51 0.40
RM154 0.59 2.00 0.49 0.37 RM316 0.98 2.00 0.03 0.03
RM327 0.57 4.00 0.58 0.52 PSM338 0.41 3.00 0.63 0.55
RM452 0.97 2.00 0.07 0.06 RM215 0.41 4.00 0.70 0.65
PSM122 0.68 3.00 0.44 0.36 PSM406 0.60 6.00 0.57 0.52
RM208 0.48 3.00 0.61 0.53 RM271 0.86 3.00 0.24 0.23
OSR13 0.97 3.00 0.07 0.07 RM171 0.88 3.00 0.22 0.20
RM338 0.91 3.00 0.16 0.15 RM484 0.69 3.00 0.47 0.42
PSM132 0.56 6.00 0.63 0.59 RM20B 0.52 3.00 0.52 0.40
RM55 0.98 2.00 0.03 0.03 RM536 0.43 4.00 0.62 0.55
RM514 0.79 2.00 0.33 0.27 RM287 0.93 3.00 0.13 0.13
PSM326 0.80 3.00 0.32 0.28 RM21 0.26 6.00 0.78 0.74
RM413 0.95 2.00 0.10 0.09 RM19 0.97 2.00 0.07 0.06
RM161 0.71 3.00 0.43 0.36 RM247 0.74 6.00 0.43 0.41
RM334 0.95 2.00 0.10 0.09 RM277 0.90 2.00 0.19 0.17
RM510 0.95 2.00 0.10 0.09 平均值Mean 0.76 3.13 0.33 0.29
RM454 0.83 2.00 0.29 0.24 最大值Max. 0.98 6.00 0.78 0.74
RM162 0.91 4.00 0.16 0.16 最小值Min. 0.26 2.00 0.03 0.03
RM11 0.95 3.00 0.10 0.10

Table 3

Genetic diversity analysis of japonica rice among different breeding units"

育种单位Breeding unit 品种数量Number of varieties Maf Na H PIC
丹东农业科学院DAAS 5 0.79abcAB 1.83bBC 0.28abA 0.23abAB
辽宁省水稻研究所LRRI 17 0.77bcB 2.44aA 0.30abA 0.26aAB
辽宁省盐碱地利用研究所LISLU 10 0.74cB 2.29aAB 0.34aA 0.30aA
辽宁省农业科学院耕作栽培研究所TCRILAAS 3 0.83abAB 1.50bcCD 0.21bcAB 0.17bcBC
沈阳农业大学SAU 17 0.82abAB 2.21aAB 0.25abAB 0.22abAB
铁岭市农业科学院TAAS 3 0.90aA 1.31cD 0.14cB 0.11cC
总体水平Total level 55 0.76 3.10 0.32 0.29

Fig.1

Cluster of japonica rices of Liaoning using NJ"

Fig.2

Cluster of breeding units using NJ"

Fig.3

The change curve of Log-likelihood function value lnP(D) and ΔK based on the K value of subgroup numbers"

Fig.4

Population structure analysis on 58 varieties The red bars and green bars represent group A and group B, respectively. (1) to (9) represent nine breeding units in sequence of TCRILAAS, LISLU, PNATDCL, LRRI, SAU, ATECDC, TAAS, DAAS, DDBF."

Fig.5

Pedigree of part rice cultivars"

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