[논문]가지속 식물의 엽록체 전장유전체 비교를 통한 PCR 기반의 Solanum demissum 특이적 분자마커 개발

박태호

doi:10.5010/jpb.2021.48.1.018

가지속 식물의 엽록체 전장유전체 비교를 통한 PCR 기반의 Solanum demissum 특이적 분자마커 개발
PCR-based markers for discriminating Solanum demissum were developed by comparison of complete chloroplast genome sequences of Solanum species 원문보기

Journal of plant biotechnology = 식물생명공학회지, v.48 no.1, 2021년, pp.18 - 25

초록
AI-Helper

멕시코로부터 유래한 Solanum demissum은 감자 야생종 중의하나로 감자 역병에 대해 저항성을 가지고 있어 감자 육종에서 중요한 재료로 이용되고 있다. S. demissum의 EBN은 4배 체인 감자와 같은 4로 직접적인 교배로 육종에 활용될 수 있다. 본 연구에서는 NGS 기술에 의해 완성된 S. demissum의 엽록체 전장 유전체(cpDNA)와 이를 다른 Solanum종과의 비교를 통해 개발한 분자마커에 대해 보고하였다. S. demissum의 전체 cpDNA의 크기는 155,558 bp였으며 그 구조는 다른 Solanum종과 매우 유사하였다. S. demissum의 cpDNA와 가지과에 속하는 10개 종의 cpDNA 코딩서열을 이용하여 분석한 계통수에서는 S. demissum이 S. hougasii 및 S. stoloniferum과 거의 동일한 유전체 구성을 보였으며, 다음으로 S. berthaultii 및 S. tuberosum과 유연관계가 가까운 것으로 확인되었다. S. demissum과 다른 7종의 Solanum과의 전체 cpDNA 다중 정렬을 통해 S. demissum 특이적인 두 개의 InDel 영역을 구명하였으며 이를 기반으로 최종적으로 PCR을 기반으로 한 두 개의 S. demissum 특이적 마커를 개발하였다. 본 연구의 결과는 Solanum 종들을 대상으로 한 조금 더 세부적인 진화적 그리고 육종적 측면에서의 연구에 기여를 할 수 있을 것이다.

Abstract ▼ AI-Helper

Solanum demissum is one of the wild Solanum species originating from Mexico. It has wildly been used for potato breeding due to its resistance to Phytophthora infestans. S. demissum has an EBN value of four, which is same as that of S. tuberosum, so that it is directly crossable for breeding purposes with the cultivated tetraploid potato (S. tuberosum). In this study, the chloroplast genome sequence of S. demissum obtained by next-generation sequencing technology was described and compared with those of seven other Solanum species to develop S. demissum-specific markers. Thetotal sequence length of the chloroplast genome is 155,558 bp, and its structural organization is similar to those of other Solanum species. Phylogenetic analysis with ten other Solanaceae species revealed that S. demissum is most closely grouped with S. hougasii and S. stoloniferum followed by S. berthaultii and S. tuberosum. Additional comparison of the chloroplast genome sequence with those of seven other Solanum species revealed two InDels specific to S. demissum. Based on these InDels, two PCR-based markers for discriminating S. demissum from other Solanum species were developed. The results obtained in this study will provide an opportunity to investigate more detailed evolutionary and breeding aspects in Solanum species.

주제어

표/그림 (7)

그림 Fig. 1 Result of assembling the complete chloroplast genome sequence of S. demissum. The four representative contigs for the chloroplast genome of S. demissum and comparison with the corresponding regions of the S. berthaultii chloroplast genome (KY419708) are combined. Blue and yellow bars indicate contig matching with the reference sequence in forward and reverse orientations, respectively
그림 Fig. 2 Gene map of the S. demissum chloroplast genome. Genes on the outside of the map are transcribed in the clockwise direction, and genes on the inside of the map are transcribed in the counterclockwise direction
표 Table 1 Results of comparative analysis of the chloroplast genome sequence of S. demissum with those of the cultivated potato, seven other Solanum species
그림 Fig. 3 Maximum-likelihood phylogenetic tree of S. demissum with eleven Solanaceae family members based on the chloroplast protein-coding sequences of each chloroplast genome. The numbers on each node indicate the bootstrap values from 1,000 replicates
그림 Fig. 4 Multiple alignment of the sequences on the intergenic regions containing InDels used to develop the PCR-based markers. The chloroplast genome sequences of S. acaule (SA11: MK036506), S. brevicaule (SB2-1: MK036507), S. demissum (SD9: MK036508), S. tuberosum (Stub: KM489056), S. commersonii (Scmr: KM489054), S. bulbocastanum (Sblb: DQ347958), S. chacoense (Scha: MF471371), and S. stoloniferum (Ssto: MF471373) were used and are listed from top to bottom in each region of the InDels. The regions of the InDels detected on that of S. demissum are bold and highlighted
그림 Fig. 5 PCR-based markers for the discrimination of S. demissum from other Solanum species. A: SD9_InDel_1. B: SD9_InDel_2. The two markers are all positively specific to S. demissum. SD7 and SD9 indicate two different lines of S. demissum (PI218047). M is a size marker ladder. SH, HR, DJ, SA, SB1, SB2, SC4, SC1, SC3, SC2, SI, SK, SJ, SM2, SM1, SP, SS, SV2, and SV1 indicate potato varieties 'Seohong', 'Haryeong', 'Daeji', S. acaule (PI310970), S. berthaultii (PI310981), S. brevicaule (PI205394), S. candolleanum (PI210035), S. cardiophyllum (PI341233), S. chacoense (PI201846), S. commersonii (PI558050), S. iopetalum (PI230459), S. kurtzianum (PI578236), S. jamesii (PI578326), S. microdontum (PI310979), S. mochiquense (PI338616), S. pinnatisectum (PI190115), S. stoloniferum (PI160224), S. vernei (PI230468) and S. verrucosum (PI160228), respectively
표 Table 2 Primers used to generate S. demissum-specific markers

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