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SNP haplotypes for soybean resistance to SCN race 1 and 3

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Abstract

Marker-assisted selection (MAS) for soybean resistance to soybean cyst nematode (SCN) is a common practice in soybean breeding programs. However, only markers associated with resistance to SCN race 3 have been used efficiently in these programs. This study aimed to identify single-nucleotide polymorphism (SNP) haplotypes associated with soybean resistance to SCN races 1 and 3, using qualitative (breeding) and quantitative (female index) approaches. A set of 169 soybean varieties were genotyped with 6000 SNP markers and phenotyped by SCN race 1 and 3 reaction. An association study was carried out by using a mixed linear model. A haplotype containing one SNP on chromosome 8 and one SNP on chromosome 18 was associated with soybean resistance to SCN race 3, and a haplotype containing the same SNP on chromosome 8 and one SNP on chromosome 11 was associated with soybean resistance to SCN race 1. For race 3, the resistance haplotype component markers were identified using the two phenotypic approaches. For race 1, the resistance haplotype was only identified using the breeding approach. The haplotype associated with race 3 identified the phenotype of resistant and susceptible varieties with accuracy of 97.4%. The same accuracy value was obtained using the haplotype associated with resistance to race 1. MAS with the haplotypes containing the SNPs on chromosomes 8 and 18 identified plants that are resistant to race 3, and sequential inclusion of the SNP on chromosome 11 identified among them those that are also resistant to race 1.

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Abbreviations

SCN:

Soybean cyst nematode

FI:

Female index

MAF:

Minimum allele frequency

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Acknowledgements

The authors thank COODETEC for support of the infrastructure and personnel required for phenotypic analyses. This project is part of CNPq Grant Projects Process 560465/2010-6, 305900/2011-0, and 482198/2010-9.

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Authors and Affiliations

  1. Universidade Paranaense (UNIPAR), Praça Mascarenhas de Moraes, 4282 - Centro, Umuarama, PR, 87502-210, Brazil

    Diorgenes Leonam Modernel da Silveira & Glacy Jaqueline da Silva

  2. Corteva Agrisciences, Rod. DF250, km 20, Brasília, DF, 73301-970, Brazil

    Tatiane Dalla-Nora Montecelli

  3. LongPing High-Tech, Rod. Anhanguera, km 330, Cravinhos, SP, 14140-000, Brazil

    Ivan Schuster

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  1. Diorgenes Leonam Modernel da Silveira
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  2. Tatiane Dalla-Nora Montecelli
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  3. Glacy Jaqueline da Silva
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  4. Ivan Schuster
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Correspondence to Ivan Schuster.

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da Silveira, D.L.M., Montecelli, T.DN., da Silva, G.J. et al. SNP haplotypes for soybean resistance to SCN race 1 and 3. Euphytica 215, 143 (2019). https://doi.org/10.1007/s10681-019-2465-7

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