Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential.

The highly significant association ( P ≤ 8.17 × 10 −5 ) between seed length to width ratio and TcSNP 733 on chromosome 5 was verified with FarmCPU ( P ≤ 1.12 × 10 −8 ).

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Consequently, the results were carefully scrutinized just below the level of significance to discern MTAs, which may also have valid functional (biological) significance and to preclude false negative MTAs associated with TASSEL MLM.

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