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RAD-based Genomic Sequencing Analysis of Jatrohpha curcas L. in Yunnan to Reveal Its Genetic Diversity
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Zhouyi ZHENG1, Yuting LIU1, Chun CHEN1, Shasha WANG1, 3, 4, *, Wei TANG1, 2, 3, *
Chinese Journal of Tropical Crops | 2023, 44(3) : 516 - 525
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Chinese Journal of Tropical Crops | 2023, 44(3): 516-525
• Germplasm Resources, Genetics & Breeding •
RAD-based Genomic Sequencing Analysis of Jatrohpha curcas L. in Yunnan to Reveal Its Genetic Diversity
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Zhouyi ZHENG1, Yuting LIU1, Chun CHEN1, Shasha WANG1, 3, 4, *, Wei TANG1, 2, 3, *
Affiliations
  • 1.School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
  • 2.Joint Academy of Potato Science, Yunnan Normal University, Kunming, Yunnan 650500, China
  • 3.Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan 650500, China
  • 4.Key Lab of Yunnan Province for Biomass Energy and Environmental Biotechnology, Kunming, Yunnan 650500, China
Published: 2023-03-25 doi: 10.3969/j.issn.1000-2561.2023.03.008
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To gain insight into the genetic diversity and relationship of the tropic bioenergy plant physic nut (Jatropha curcas L.) in Yunnan, China, joint analysis of agronomic and molecular characters was performed in the present study, using different accessions collected from nine sources/geographical provenances in Yunnan. To investigate the population polymorphism, eight pairs of SSR molecular markers were developed by MISA program, and four of them with higher polymorphism were selected for PCR amplification using 95 DNA samples collected from nine populations. The results indicated that JC01 exhibited the best polymorphism (0.711). UPGMA clustering analysis suggested that Baoshan and Xishuangbanna might serve as the parents or origins of physic nut in Yunnan, which was partially related to the geographical origin of populations. Comprehensive investigations revealed among all examined biological traits of seeds or seedlings, the underground fresh weight (UFW) exhibited the highest coefficient of variation, with obvious separation among populations. Two individual seedlings with extreme variance in UFW (BNMH and CXYM) were selected for RAD-based genomic sequencing, while 2783 and 3033 contigs were assembled. Analysis of genome assembly data using GenomeScope revealed that both materials were diploid, and a total 22 756 valid SNPs were detected at the whole genome level using genome-wide association study (GWAS). High frequency-SNPs associated with UFW preferably located on LG9, and three candidate proteins were linked to the UFW trait. The results indicated that the physic nut germplasm collected from different regions of Yunnan exhibited a high level of genetic diversity and uniqueness, which should facilitate further studies on its molecular breeding.

physic nut (Jatropha curcas L.)  /  genetic diversity  /  molecular markers  /  GWAS  /  SNP
Zhouyi ZHENG, Yuting LIU, Chun CHEN, Shasha WANG, Wei TANG. RAD-based Genomic Sequencing Analysis of Jatrohpha curcas L. in Yunnan to Reveal Its Genetic Diversity[J]. Chinese Journal of Tropical Crops, 2023 , 44 (3) : 516 -525 . DOI: 10.3969/j.issn.1000-2561.2023.03.008
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Year 2023 volume 44 Issue 3
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Article Info
doi: 10.3969/j.issn.1000-2561.2023.03.008
  • Receive Date：2022-06-07
  • Online Date：2026-03-05
  • Published：2023-03-25
Article Data
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History
  • Received：2022-06-07
  • Revised：2022-07-06
Funding
Affiliations
    1.School of Life Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
    2.Joint Academy of Potato Science, Yunnan Normal University, Kunming, Yunnan 650500, China
    3.Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan 650500, China
    4.Key Lab of Yunnan Province for Biomass Energy and Environmental Biotechnology, Kunming, Yunnan 650500, China
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https://castjournals.cast.org.cn/joweb/rdzwxb/EN/10.3969/j.issn.1000-2561.2023.03.008
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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