Korean Journal of Plant Resources (한국자원식물학회지)

The Plant Resources Society of Korea (한국자원식물학회)
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Construction of Database System on Amylose and Protein Contents Distribution in Rice Germplasm Based on NIRS Data

벼 유전자원의 아밀로스 및 단백질 성분 함량 분포에 관한 자원정보 구축

  • Oh, Sejong (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Choi, Yu Mi (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Lee, Myung Chul (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Lee, Sukyeung (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Yoon, Hyemyeong (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Rauf, Muhammad (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Chae, Byungsoo (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA)
  • 오세종 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • 최유미 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • 이명철 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • 이수경 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • 윤혜명 (농촌진흥청 국립농업과학원 농업유전자원센터) ;
  • ;
  • 채병수 (농촌진흥청 국립농업과학원 농업유전자원센터)
  • Received : 2019.02.26
  • Accepted : 2019.03.21
  • Published : 2019.04.30
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Abstract

This study was carried out to build a database system for amylose and protein contents of rice germplasm based on NIRS (Near-Infrared Reflectance Spectroscopy) analysis data. The average waxy type amylose contents was 8.7% in landrace, variety and weed type, whereas 10.3% in breeding line. In common rice, the average amylose contents was 22.3% for landrace, 22.7% for variety, 23.6% for weed type and 24.2% for breeding line. Waxy type resources comprised of 5% of the total germplasm collections, whereas low, intermediate and high amylose content resources share 5.5%, 20.5% and 69.0% of total germplasm collections, respectively. The average percent of protein contents was 8.2 for landrace, 8.0 for variety, and 7.9 for weed type and breeding line. The average Variability Index Value was 0.62 in waxy rice, 0.80 in common rice, and 0.51 in protein contents. The accession ratio in arbitrary ranges of landrace was 0.45 in amylose contents ranging from 6.4 to 8.7%, and 0.26 in protein ranging from 7.3 to 8.2%. In the variety, it was 0.32 in amylose ranging from 20.1 to 22.7%, and 0.51 in protein ranging from 6.1 to 8.3%. And also, weed type was 0.67 in amylose ranging from 6.6 to 9.7%, and 0.33 in protein ranging from 7.0 to 7.9%, whereas, in breeding line it was 0.47 in amylose ranging from 10.0 to 12.0%, and 0.26 in protein ranging from 7.0 to 7.9%. These results could be helpful to build database programming system for germplasm management.

본 연구는 선행연구에서 개발된 근적외선 분광법(NIRS) 예측모델을 활용하여 농업유전자원센터에서 보존 중인 국내외 벼유전자원의 아밀로스 및 단백질 함량 자료를 통계 처리하여 자원 분포를 파악하기 위한 데이터베이스를 구축하고자 하였다. 예측모델의 $R^2$ 값은 아밀로스 분석결과 0.970이었고, 단백질은 0.983이었다. 미지시료 측정 시 정확도를 평가하기 위해 외부검정과정을 거친 결과 $R^2$ 값은 아밀로스 분석결과 0.962였고, 단백질은 0.986이었다. 벼 자원을 재래종, 육성품종, 잡초형, 육성계통으로 나누어 NIRS를 이용하여 성분 분석한 후 함량분포를 확인하였다. 찰벼 평균 아밀로스는 재래종, 육성품종, 잡초형에서 동일하게 8.7%였고, 육성계통은 10.3%였다. 메벼 평균 아밀로스는 재래종 22.3%, 육성품종 22.7%, 잡초형 23.6%, 육성계통 24.2%였다. 전체 벼 자원 중 아밀로스 함량 9%이하 waxy type은 5.0%, low amylose는 5.5%, middle amylose는 20.5%, high amylose는 69.0%를 차지하였다. 단백질 분석 결과 평균함량은 재래종 8.2%, 육성품종 8.0%, 잡초형 7.9%, 육성계통 7.9%였다. 찰벼의 다양성지수 평균은 0.62, 메벼는 0.80이었고, 단백질 다양성지수는 평균 0.51이었다. 임의의 함량구간 내 자원비율은 정규분포의 표준화과정을 통해 확인하였다. 임의 구간에 대한 자원분포비율 산출 결과는, 재래종 아밀로스 6.4-8.7% 구간의 자원비율은 0.45였고, 22.3-26.1% 구간은 0.40, 단백질 7.3-8.2% 구간은 0.26이었다. 육성품종 아밀로스 8.7-9.4% 구간의 자원비율은 0.19였고, 20.1-22.7% 구간은 0.32, 단백질 6.1-8.3% 구간은 0.51이었다. 잡초형 아밀로스 6.6-9.7% 구간은 0.67이었고, 23.6-24.8% 구간은 0.19, 단백질 7.0-7.9% 구간은 0.33이었다. 육성계통 아밀로스 10.0-12.0% 구간의 자원비율은 0.47이었고, 24.2-28.0% 구간은 0.40, 단백질 7.0-7.9% 구간은 0.26이었다. 어떤임의 구간을 지정하여도 자원의 비율을 쉽게 구할 수 있으며, NIRS 분석과 통계분석과정을 통해 얻어진 자원별, 성분함량별 특성 자료는 효율적인 자원관리를 위한 데이터베이스 시스템 구축을 위한 기초 자료로 활용될 수 있을 것으로 판단된다.

Keywords

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Fig. 1. Relationship between probability density histogram and normal distribution.

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Fig. 2. The process and findings of standardization of normal distribution.

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Fig. 3. Outputting number of accessions in random data range by standardization of normal distribution.

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Fig. 4. Correlation plots between NIRS data and amylose (A) and protein content (B) in the milled brown rice germplasm.

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Fig. 5. Normal distribution and probability density of amylose content in landrace (A1, A2), rice variety (B1, B2), weed type (C1, C2) and breeding line (D1, D2) germplasm.

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Fig. 6. Normal distribution and probability density of protein content in landrace (A), rice variety (B), weed type (C) and breeding line (D) germplasm.

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Fig. 7. Number of accessions obtained from the probability density using the process of standard normal distribution of waxy type amylose content in landrace (n=688).

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Fig. 8. Number of accessions obtained from the probability density using the process of standard normal distribution of common rice amylose content in landrace (n=4,260).

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Fig. 9. Number of accessions obtained from the probability density using the process of standard normal distribution of protein content in landrace (n=4,948).

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Fig. 10. Number of accessions obtained from the probability density using the process of standard normal distribution of waxy type amylose content in rice variety (n=617).

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Fig. 11. Number of accessions obtained from the probability density using the process of standard normal distribution of common rice amylose content in rice variety (n=5,540).

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Fig. 12. Number of accessions obtained from the probability density using the process of standard normal distribution of protein content in rice variety (n=6,157).

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Fig. 13. Number of accessions obtained from the probability density using the process of standard normal distribution of waxy type amylose content in weed type (n=418).

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Fig. 14. Number of accessions obtained from the probability density using the process of standard normal distribution of common rice amylose content in weed type (n=5,788).

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Fig. 15. Number of accessions obtained from the probability density using the process of standard normal distribution of protein content in weed type (n=6,206).

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Fig. 16. Number of accessions obtained from the probability density using the process of standard normal distribution of waxy type amylose content in breeding line (n=596).

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Fig. 17. Number of accessions obtained from the probability density using the process of standard normal distribution of common rice amylose content in breeding line (n=9,402).

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Fig. 18. Number of accessions obtained from the probability density using the process of standard normal distribution of protein content in breeding line (n=9,998).

Table 1. Origin distribution of rice germplasm used in the analysis of NIRS

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Table 2. External validation results of NIRS equation model for the amylose and protein content in the milled brown rice

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Table 3. Classification of rice germplasm according to amylose content by NIRS

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