Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers
To better understand the genetic diversity and population structure of broccoli cultivars planted in China, a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism (SNP) markers. Ten pairs of primers with good polymorp...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2021-09-01
|
| Series: | Horticultural Plant Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014121000716 |
| _version_ | 1797203620952801280 |
|---|---|
| author | Jingjing Huang Yumei Liu Fengqing Han Zhiyuan Fang Limei Yang Mu Zhuang Yangyong Zhang Honghao Lv Yong Wang Jialei Ji Zhansheng Li |
| author_facet | Jingjing Huang Yumei Liu Fengqing Han Zhiyuan Fang Limei Yang Mu Zhuang Yangyong Zhang Honghao Lv Yong Wang Jialei Ji Zhansheng Li |
| author_sort | Jingjing Huang |
| collection | DOAJ |
| description | To better understand the genetic diversity and population structure of broccoli cultivars planted in China, a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism (SNP) markers. Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions (inbred lines) with different phenotypes and maturity. The 10 pairs of SNP primers were selected, producing 78 alleles. The diversity analysis indicated that the polymorphism information content (PIC) of SNP primer ranged from 0.64 to 0.90. The observed number of alleles (Na) was 2.00, the effective number of alleles (Ne) was 1.11–2.00, the Nei's gene diversity (H) was 0.10–0.50, and Shannon information index (I) was 0.20–0.70 using PopGene32 software. The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups (A, B, C and D), foreign cultivars were all assigned to subgroup A, and domestic cultivars were assigned to 3 subgroups of B, C, and D. This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background, but most domestic cultivars were still different from the Japanese cultivars. When K = 2, the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group (2 groups) and 1 mixed group. When Q ≥ 0.6, 143(88.82%) broccoli cultivars belonged to the simple groups. In simple groups 68 (42.24%) broccoli cultivars of group 1 were derived from Japan, the United States, Switzerland, the Netherlands, China-Taiwan, and China-Mainland; 75 (46.58%) broccoli cultivars belonged to group 2; when Q < 0.6, 18 (11.18%) broccoli cultivars belonged to the mixed groups. This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide, which is beneficial to plant breeding and materials innovation. And meanwhile, this result is also used for construction of broccoli fingerprint serving for cultivar identification. |
| first_indexed | 2024-04-24T08:22:14Z |
| format | Article |
| id | doaj.art-253588d2c8124612bbd75420d6f9df0e |
| institution | Directory Open Access Journal |
| issn | 2468-0141 |
| language | English |
| last_indexed | 2024-04-24T08:22:14Z |
| publishDate | 2021-09-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Horticultural Plant Journal |
| spelling | doaj.art-253588d2c8124612bbd75420d6f9df0e2024-04-17T00:26:50ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412021-09-0175423433Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markersJingjing Huang0Yumei Liu1Fengqing Han2Zhiyuan Fang3Limei Yang4Mu Zhuang5Yangyong Zhang6Honghao Lv7Yong Wang8Jialei Ji9Zhansheng Li10Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaInstitute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaCorresponding author. Tel: +86 10 62135629; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Beijing 100081, ChinaTo better understand the genetic diversity and population structure of broccoli cultivars planted in China, a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism (SNP) markers. Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions (inbred lines) with different phenotypes and maturity. The 10 pairs of SNP primers were selected, producing 78 alleles. The diversity analysis indicated that the polymorphism information content (PIC) of SNP primer ranged from 0.64 to 0.90. The observed number of alleles (Na) was 2.00, the effective number of alleles (Ne) was 1.11–2.00, the Nei's gene diversity (H) was 0.10–0.50, and Shannon information index (I) was 0.20–0.70 using PopGene32 software. The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups (A, B, C and D), foreign cultivars were all assigned to subgroup A, and domestic cultivars were assigned to 3 subgroups of B, C, and D. This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background, but most domestic cultivars were still different from the Japanese cultivars. When K = 2, the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group (2 groups) and 1 mixed group. When Q ≥ 0.6, 143(88.82%) broccoli cultivars belonged to the simple groups. In simple groups 68 (42.24%) broccoli cultivars of group 1 were derived from Japan, the United States, Switzerland, the Netherlands, China-Taiwan, and China-Mainland; 75 (46.58%) broccoli cultivars belonged to group 2; when Q < 0.6, 18 (11.18%) broccoli cultivars belonged to the mixed groups. This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide, which is beneficial to plant breeding and materials innovation. And meanwhile, this result is also used for construction of broccoli fingerprint serving for cultivar identification.http://www.sciencedirect.com/science/article/pii/S2468014121000716BroccoliGenetic diversity;Population structure analysis;FingerprintSNP |
| spellingShingle | Jingjing Huang Yumei Liu Fengqing Han Zhiyuan Fang Limei Yang Mu Zhuang Yangyong Zhang Honghao Lv Yong Wang Jialei Ji Zhansheng Li Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers Horticultural Plant Journal Broccoli Genetic diversity;Population structure analysis;Fingerprint SNP |
| title | Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers |
| title_full | Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers |
| title_fullStr | Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers |
| title_full_unstemmed | Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers |
| title_short | Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers |
| title_sort | genetic diversity and population structure analysis of 161 broccoli cultivars based on snp markers |
| topic | Broccoli Genetic diversity;Population structure analysis;Fingerprint SNP |
| url | http://www.sciencedirect.com/science/article/pii/S2468014121000716 |
| work_keys_str_mv | AT jingjinghuang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT yumeiliu geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT fengqinghan geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT zhiyuanfang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT limeiyang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT muzhuang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT yangyongzhang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT honghaolv geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT yongwang geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT jialeiji geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers AT zhanshengli geneticdiversityandpopulationstructureanalysisof161broccolicultivarsbasedonsnpmarkers |