Abstract
Key Message
The use of multi-environment trials to test yield-related traits in a diverse alfalfa panel allowed to find multiple molecular markers associated with complex agronomic traits.
Abstract
Yield is one of the most important target traits in alfalfa breeding; however, yield is a complex trait affected by genetic and environmental factors. In this study, we used multi-environment trials to test yield-related traits in a diverse panel composed of 200 alfalfa accessions and varieties. Phenotypic data of maturity stage measured as mean stage by count (MSC), dry matter content, plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses were used to obtain estimated trait means of entries by environment. The plants were genotyped using a genotyping by sequencing approach and obtained a genotypic matrix with 97,345 single nucleotide polymorphisms. Genome-wide association studies identified a total of 84 markers associated with the traits analyzed. Of those, 29 markers were in noncoding regions and 55 markers were in coding regions. Ten significant SNPs at the same locus were associated with FD and they were linked to a gene annotated as a nuclear fusion defective 4-like (NFD4). Additional SNPs associated with MSC, PH, and Yi were annotated as transcription factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and serine/threonine-protein phosphatase 7 proteins, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed up the genetic gain toward alfalfa yield improvement.
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Data availability
The raw sequencing data has been submitted to NCBI with Sequence Read Archive (SRA) Project #PRJNA666630. The phenotypic, genotypic datasets and R codes generated during study are available in the Figshare repository, https://doi.org/10.6084/m9.figshare.21712106.
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Acknowledgements
We thank Dr. Edzard van Santen for his efforts on the field design.
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This work was supported by Alfalfa Forage Research Program (AFRP) from National Institute of Food and Agriculture (NIFA) under grant project number: WN.N1678, Determining genetic factors that influence forage quality in alfalfa.
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LXY and SN conceived this study. SL and CM performed the genetic and association analysis. CM, SL, and LXY wrote the manuscript. SN, DC, GW, GS, SF, and DL conducted field trials and collected the phenotypic data from each location.
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Lin, S., Medina, C.A., Wang, G. et al. Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials. Theor Appl Genet 136, 121 (2023). https://doi.org/10.1007/s00122-023-04364-4
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DOI: https://doi.org/10.1007/s00122-023-04364-4