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Background  Observations of precocious (early bearing) genotypes of walnut ( Juglans regia  L.) under natural conditions encouraged us to study the origin and genetic control of these fascinating traits.    Results  In this study, the self-fertility, progeny performance, and simple sequence repeat (SSR) locus variation of iron walnut ( Juglans sigillata  Dode), an ecotype of  J. regia , were investigated. The average self-pollinated fruit set rate of  J. sigillata  cv. ‘Dapao’ (DP) was 7.0% annually from 1979 to 1982. The average germination rate of self-pollinated seeds was 45.2% during the 4-year period. Most progeny had inbreeding depression. Nine representative self-pollinated progeny (SP 1 –SP 9 ), with special or typical traits of DP, were selected. SP 1 –SP 4  were precocious because they initiated flowers as early as 2 years after germination, compared to the 7–10-yr period that is typical of DP. SP 9  had not flowered since 1980. Twelve SSR markers were used to analyze the SP and DP. The genome of SP had a tendency toward high levels of homozygosity. The high levels of homozygosity reported in 18 additional precocious walnut genotypes complemented the results of this study.    Conclusions  These results provide evidence of precocious phenotypes and genomes with high levels of homozygosity that might be generated from self-pollinating walnut. This suggests that self-pollination might facilitate the generation of unique homozygous parents for subsequent use in walnut-breeding programs. The results also indicate that more attention should be focused on adequate management of precocious walnut to avoid early depression in the production of nuts.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1549-1) contains supplementary material, which is available to authorized users.

Precocious genotypes and homozygous tendency generated by self-pollination in walnut