Meristems are central to plant growth and development, yet evidence of directly manipulating this control to improve crop yield is scarce. Kernel row number (KRN) is an important agronomic trait that can directly affect maize (Zea mays L.) yield. However, this trait is difficult to select by phenotyping, since it is highly variable in the mixed genetic backgrounds in early selfing generations. This study sought to improve this trait by marker-assisted backcrossing (MABC) of a weak allele of FASCIATED EAR 2 that is known to affect inflorescence meristem size, but the effect of which on yield is unclear. All of the four introgressed tropical elite inbreds of different heterotic groups, which are homozygous for the fea2-1328 allele, had 2–5 more KRNs compared to their respective recurrent parents. Furthermore, one hybrid made from crosses between two introgressed parents also had KRN increases that resulted in up to 28% yield increase compared to the original hybrid across multiple yield trials. The novel negative effects of the pericentromeric fea2 and/or its linkage drag effect on plant height, seed weight, and ear length, which could prevent line improvement, were revealed in several genetic backgrounds. Integration of conventional phenotypic selection to overcome these undesirable effects was discussed. This is the first work to demonstrate the possibility to increase yield of maize varieties using a mutation in a meristem size regulator. The crossing, selection strategies, and recombinant lines in this work can be applied to other elite maize hybrids and provide a potentially straightforward, non-transgenic way to improve the yield of an existing variety by 8–28%.

Black soybean is an important functional crop valued for its high anthocyanin content and associated health benefits, attracting increasing interest in plant breeding and mutation-based approaches to enhance its nutritional and agronomic traits. Here, we investigated a DT26 black seed-coat mutant (DT26BS) derived from the Vietnamese cultivar DT26 following gamma irradiation. Genetic analysis of F₂ populations indicated that the phenotype is controlled by a single recessive mutation, with additional epistatic interactions observed in other genetic backgrounds. MutMap analysis based on whole-genome sequencing of pooled F₂ individuals identified a candidate region on chromosome 8 corresponding to the I locus. A large deletion (~176 kb) was identified in this region, affecting multiple Chalcone Synthase (CHS) gene repeats, and which may disrupt RNAi-mediated silencing of CHS, thereby triggering anthocyanin restoration in the seed coat. PCR-based markers confirmed tight linkage between this deletion and the black seed-coat phenotype. Crosses with elite lines and further selection until F7 generations showed that the mutation has no adverse effects on major agronomic traits and is useful as a donor for developing improved lines with black seed coat, shorter maturity, high yield, and enhanced anthocyanin content for nutritional improvement. These results demonstrate the utility of MutMap for detecting irradiation-induced structural variants and extend its application to a non-reference elite tropical soybean background, providing a useful genetic resource for black soybean breeding.