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Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population

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A multiparental random mating population used in sorghum breeding is amenable for the detection of QTLs related to tropical soil adaptation, fine mapping of underlying genes and genomic selection approaches.

Abstract

Tropical soils where low phosphorus (P) and aluminum (Al) toxicity limit sorghum [Sorghum bicolor (L.) Moench] production are widespread in the developing world. We report on BRP13R, a multiparental random mating population (MP-RMP), which is commonly used in sorghum recurrent selection targeting tropical soil adaptation. Recombination dissipated much of BRP13R’s likely original population structure and average linkage disequilibrium (LD) persisted up to 2.5 Mb, establishing BRP13R as a middle ground between biparental populations and sorghum association panels. Genome-wide association mapping (GWAS) identified conserved QTL from previous studies, such as for root morphology and grain yield under low-P, and indicated the importance of dominance in the genetic architecture of grain yield. By overlapping consensus QTL regions, we mapped two candidate P efficiency genes to a ~ 5 Mb region on chromosomes 6 (ALMT) and 9 (PHO2). Remarkably, we find that only 200 progeny genotyped with ~ 45,000 markers in BRP13R can lead to GWAS-based positional cloning of naturally rare, subpopulation-specific alleles, such as for SbMATE-conditioned Al tolerance. Genomic selection was found to be useful in such MP-RMP, particularly if markers in LD with major genes are fitted as fixed effects into GBLUP models accommodating dominance. Shifts in allele frequencies in progeny contrasting for grain yield indicated that intermediate to minor-effect genes on P efficiency, such as SbPSTOL1 genes, can be employed in pre-breeding via allele mining in the base population. Therefore, MP-RMPs such as BRP13R emerge as multipurpose resources for efficient gene discovery and deployment for breeding sorghum cultivars adapted to tropical soils.

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Acknowledgements

We acknowledge grants from the CGIAR Generation Challenge Program, the Embrapa Macroprogram, the Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG) and the National Council for Scientific and Technological Development (CNPq). The funding body had no role in the design of the study and collection, analysis and interpretation of data and in writing the manuscript. We also thank Gislene Braga Cristeli and all the staff and trainees of Embrapa Maize and Sorghum that indirectly collaborated in the execution of this work.

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Authors and Affiliations

  1. Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG, 36570-900, Brazil

    Karine C. Bernardino & Pedro C. S. Carneiro

  2. Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil

    Karine C. Bernardino, Cícero B. de Menezes, Sylvia M. de Sousa, Claudia T. Guimarães, Robert E. Schaffert, Barbara Hufnagel, Maria Marta Pastina & Jurandir V. Magalhaes

  3. Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada

    Leon V. Kochian

  4. BPMP, CNRS, INRAE, SupAgro, University of Montpellier, 34060, Montpellier, France

    Barbara Hufnagel

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  1. Karine C. Bernardino
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  2. Cícero B. de Menezes
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  3. Sylvia M. de Sousa
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  9. Maria Marta Pastina
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  10. Jurandir V. Magalhaes
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Contributions

JVM conceived, supervised the study and contributed to manuscript writing and revision, KCB performed experiments, analyzed the data and contributed to manuscript writing, CBM, SMS and RES contributed to sorghum phenotyping, MMP designed the statistical framework and contributed to data analysis and interpretation, BH contributed to integrative analysis of QTL conservation between RILs and BRP13R, LVK, CTG and PCSC revised the manuscript, and all authors read and approved the final manuscript.

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Correspondence to Maria Marta Pastina or Jurandir V. Magalhaes.

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Communicated by Hai-Chun Jing.

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Bernardino, K.C., de Menezes, C.B., de Sousa, S.M. et al. Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population. Theor Appl Genet 134, 295–312 (2021). https://doi.org/10.1007/s00122-020-03697-8

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