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Leaf shape, texture, and size variability in sugar beet breeding lines and associated single nucleotide polymorphisms using a genome-wide association analysis

genetics
plant-science

Abstract

Background. Sugar beet leaf morphology and plant architecture have largely been unselected over the past 150 years of breeding. Yet leaf characteristics and plant architecture have an impact on canopy closure and air flow, light capture, and ultimately sucrose accumulation in roots.

Method. Using greenhouse-grown plants, we evaluated leaf morphology [e.g., color, size, and shape] for 252 sugar beets representing 27 heterogeneous genotypes and 16 genetic families from the USDA ARS East Lansing sugar beet breeding program. Low-coverage, short-read sequencing was performed on 263 individuals for genome-wide associations.

Results. Significant variability was observed within and among beet accessions and families for total leaf area, width, length, shape, and color. More than 70% of the observed leaf shape variation was explained by two principal components, and leaves were further grouped into six shape-related clusters using k-means clustering. Greatest variability in shape was observed along the base of the leaves near the petiole attachment and the upper 1/3 of the leaf blade. Using a genome-wide association approach, large and small effect SNPs associated with leaf area, shape, color, undulate margins, and crinkled blades were identified. Major SNPs associated with shape were associated with chromosomes 1, 5, and 8. Major SNPs associated with color traits were found on chromosomes 1, 3, 4, and 7. Leaf crinkles or undulate margins were primarily associated with SNPs found on chromosomes 4, 6, and 9.

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