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Zhiyang WU, Dan ZONG, Peihua GAN, et al. Genetic Analysis on Different Stem Forms of Pinus yunnanensis by Reduced-representation Genome Sequencing[J]. JOURNAL OF YUNNAN AGRICULTURAL UNIVERSITY（Natural Science）, 2022, 37(2): 285-293. DOI: 10.12101/j.issn.1004-390X(n).202108048
Citation: Zhiyang WU, Dan ZONG, Peihua GAN, et al. Genetic Analysis on Different Stem Forms of Pinus yunnanensis by Reduced-representation Genome Sequencing[J]. JOURNAL OF YUNNAN AGRICULTURAL UNIVERSITY（Natural Science）, 2022, 37(2): 285-293. DOI: 10.12101/j.issn.1004-390X(n).202108048
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Genetic Analysis on Different Stem Forms of Pinus yunnanensis by Reduced-representation Genome Sequencing

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    • Abstract
  • PurposeTo study the genetic differences between straight and twisted stems of Pinus yunnanensis, revealing its genetic variation characteristics.
    MethodEndosperm and needles of total 22 samples used as materials, reduced-representation genome sequencing technology was employed to develop single nucleotide polymorphism (SNP) markers and analyze genetic differences between straight and twisted stems of P. yunnanensis.
    ResultsAfter detection of genetic variation, a total of 772 240 variable sites were obtained. Of which, 762 699 variable sites were SNPs, and the variation type of transversion (38.28%) was lower than that of transitions (61.72%); 9 541 variable sites were InDels, and the variation type of insertion and deletion were roughly equal. Genetics analyses results showed that: among endosperm group in straight stem (ES), needle group in straight stem (NS), endosperm group in twisted stem (ET) and needle group in twisted stem (NT), the polymorphism information content (PIC), Nei ’s diversity index (Nei) and the information index of Shannon (I) ranged from 0.163 3 to 0.183 7, 0.234 5 to 0.262 5 and 0.304 3 to 0.344 8, respectively. These genetic variation indexes indicated that there were lower levels of genetic variation in tested samples of P. yunnanensis. However, there was moderate genetic differentiation (Fst-needle=0.107 1, Fst-endosperm=0.143 7) and frequent gene flow (Nm-needle=2.083 9, Nm-endosperm=1.489 3) between straight and twisted stems of P. yunnanensis. Furthermore, straight and twisted stems of P. yunnanensis could be completely identified by 39 SNPs located in 27 selected sequences. The SNP annotation results suggested that pleiotropic drug resistance protein 3 (PDR3), ethylene-responsive transcription factors (ERF017 and RAP2) and MYB-related protein 340 (MYB340) maybe played a role in the regulation on straight and twisted stems development of P. yunnanensis.
    ConclusionThe main stem twisted variation of P. yunnanensis is mainly regulated by genetic factors, but the synergistic effect of environmental factors enhances the significance of this feature.
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