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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (11): 2876-2885.doi: 10.3724/SP.J.1006.2023.23066

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Application of maize 6H-60K chip in identification of maize essentially derived varieties

TIAN Hong-Li(), ZHANG Ru-Yang(), FAN Ya-Ming(), YANG Yang, ZHANG Yun-Long, YI Hong-Mei, XING Jin-Feng, WANG Feng-Ge(), ZHAO Jiu-Ran()   

  1. Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences / Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province) / Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097, China
  • Received:2022-09-30 Accepted:2023-05-24 Online:2023-11-12 Published:2023-06-06
  • About author:First author contact:

    **Contributed equally to this study

  • Supported by:
    National Scientific and Technological Innovation—Major Projects(2022ZD04019);Science and Technology Innovation Capacity Building Project of BAAFS (KJCX20230301)(KJCX202303)

Abstract:

The identification of maize essentially derived variety has become the hot spot in the intellectual property protection of seed industry. In order to speed up the establishment of its accurate and efficient molecular identification technology, this article used multiple types of derived varieties as research materials: Jing 2416 and Jing 2416C (two inbred lines with highly similar genetic backgrounds), Jing 724 and Jing 72464 (two inbred lines with similar genetic backgrounds), as well as 893 DH lines of genetic population constructed by Jing 724 and Jing 72464. The study researched and analyzed the potential of maize 6H-60K chip including 61,214 SNPs in identification of maize essentially derived varieties. The results were as follows: (1) There were 829 SNPs differences between Jing 2416 and Jing 2416C, the GS value (genetic similarity) was 98.7%, and 56.7% of the difference loci were concentrated in the 39 Mb region of chromosome 5. (2) There were 4912 SNPs differences between Jing 724 and Jing 72464, the GS value was 90.1%, and 44.8% of the difference loci were concentrated on chromosome 3. (3) The distribution of genetic similarity values between 893 DH lines and two parents (Jing 724 and Jing 72464) was continuous. The GS value range between 893 DH lines and Jing 724 was 88.0%-97.0%, with an average of 92.6%. The GS value range between 893 DH lines and Jing 72464 was 88.3%-98.6%, with an average of 94.5%. (4) 893 DH lines were paired comparison, a total of 398,278 pairs were compared. There were specific SNP differences between all DH lines. The GS values of 893 DH lines in pairs ranged from 87.5% to 99.9%, with an average of 94.3%. Among them, the proportion of GS value ≥ 97.0% was 8.6%, and the proportion of GS value ≥ 99.0% was 1.3%. This study showed that maize 6H-60K SNP sets could accurately evaluate the genetic background of maize derived, similar or extremely similar inbred and DH lines, identify and distinguish all materials one by one, and had the potential to further lock the linkage markers of derived traits. It is suggested that the technical system for maize essentially derived variety molecular identification based on Maize6H-60K SNP sets using chip, genotyping by target sequencing (GBTS) and other platforms should be urgently established, so as to provide technical support for intellectual property protection and variety innovation of maize varieties.

Key words: maize, the essentially derived variety, molecular identification, maize 6H-60K chip, the high-density SNP loci set

Fig. 1

Distribution of different loci between Jing 2416 and Jing 2416C in the whole genome"

Fig. 2

Distribution of different loci between Jing 724 and Jing 72464 in the whole genome (A and B), and recombinant frequency of 10 chromosomes based on DH lines groups (C)"

Fig. 3

Genetic similarity analysis between each DH line and Jing 724 and Jing 72464 The abscissa is the 893 DH lines, sorted from small to large according to the LS value with Jing 72464. The ordinate is the genetic similarity value."

Fig. 4

Distribution of genetic similarity between two DH lines of 893 DH lines The abscissa is the value of genetic similarity and locus similarity, and the ordinate is the number of paired analysis DH lines."

Fig. 5

Genetic segregation of DH line population constructed by Jing 724 and Jing 72464 Fig. A is the genetic segregation diagram of polymorphic markers, red is the partial maternal segregation loci, and the orange is the unbiased segregation loci. Figs. B, C, and D are genetic background of three DH lines (DH388, DH677, and DH543). Genotypes are indicated as follows: white area, the same homozygous genotype as Jing 724 and Jing 72464; green, the same homozygous genotype as Jing 724; red, the same homozygous genotype as Jing 72464."

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