Abstract
• The distribution and structural features of simple repeat sequences in chestnut were clarified at the genome-wide level. • A highly universal and polymorphic SSR marker database was created using cross species resequencing data. • The newly developed SSR markers were used to draw DNA molecular identification cards for ancient chestnut resources in northern China, thereby providing scientific support for the protection and utilization of chestnut resources in the future. Chinese chestnut is an important economic forest tree species with enormous application value in the wood, medical, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38 Mb –1 . Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were ultimately obtained. To verify the capability of the developed SSR for identification, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains. The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have good potential for identification. We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species. The molecular markers amplified 94% of the interspecies with a polymorphic information content (PIC) value of 0.859. Cluster analysis revealed that the resources can be well differentiated using these developed markers, and these markers can be widely used to identify interspecific boundaries. The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, the selection of good products, and the construction of core germplasm resources of chestnut and even chestnut plants. Also these markers provide a solid foundation for the molecular design of hybrids, improved breeding and development of germplasm resources.
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Claims 8
Claim · model-written summary
A total of 312,302 SSR molecular markers were identified across the Chinese chestnut genome
- Taxon
- Chinese chestnut
Castanea mollissimae0 - Outcome
- molecular markerse1
- Value
- 312,302e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chinese chestnut is an important economic forest tree species”
e1“A total of 312,302 molecular markers were obtained with a density of 434.38 Mb –1”
Claim · model-written summary
After polymorphism screening, 138,208 polymorphic SSR loci were obtained in Chinese chestnut
- Taxon
- Chinese chestnutCastanea mollissimae0
- Outcome
- polymorphic locie2
- Value
- 138,208e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chinese chestnut is an important economic forest tree species”
e2“138,208 polymorphic loci were ultimately obtained”
Claim · model-written summary
Only six primer pairs were required to create a unique DNA fingerprint of ancient chestnut trees
- Taxon
- Chinese chestnutCastanea mollissimae0
- Material
- ancient treese3
- Outcome
- unique DNA fingerprinte3
- Value
- six pairs of primerse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chinese chestnut is an important economic forest tree species”
e3“only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees”
Claim · model-written summary
The developed SSR markers amplified 94% of interspecies Castanea samples
CastaneaOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“91 Castanea plants of three different species”
e4“The molecular markers amplified 94% of the interspecies with a polymorphic information content (PIC) value of 0.859”
Claim · model-written summary
The developed SSR markers had a polymorphic information content of 0.859 in Castanea
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“91 Castanea plants of three different species”
e4“The molecular markers amplified 94% of the interspecies with a polymorphic information content (PIC) value of 0.859”
Claim · model-written summary
Cluster analysis showed that Castanea resources can be well differentiated with the developed markers
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e6“91 Castanea plants of three different species”
e5“Cluster analysis revealed that the resources can be well differentiated using these developed markers”
Claim · model-written summary
The developed markers can be widely used to identify interspecific boundaries in Castanea (author recommendation)
- Outcome
- identify interspecific boundariese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e7“91 Castanea plants of three different species”
e6“these markers can be widely used to identify interspecific boundaries”
Claim · model-written summary
The developed markers have potential for assessing genotypic diversity in chestnut (author interpretation)
- Taxon
- Chinese chestnutCastanea mollissimae0
- Outcome
- assessing genotypic diversitye7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Chinese chestnut is an important economic forest tree species”
e7“the developed molecular markers have the potential for assessing genotypic diversity”