Grain number is an important factor in determining grain production of rice (Oryza sativa L.). The molecular genetic basis for grain number is complex. Discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. Here, we identified GRAINS NUMBER 2 (GN2), a novel gene that is responsible for rice grain number, from “Yuanjiang” common wild rice (O. rufipogon Griff.). Transgenic plants overexpressing GN2 showed less grain number, reduced plant height, and later heading date than control plants. Interestingly, GN2 arose through the insertion of a 1094-bp sequence from LOC_Os02g45150 into the third exon of LOC_Os02g56630, and the inserted sequence recruited its nearby sequence to generate the chimeric GN2. The gene structure and expression pattern of GN2 were distinct from those of LOC_Os02g45150 and LOC_Os02g56630. Sequence analysis showed that GN2 may be generated in the natural population of Yuanjiang common wild rice. In this study, we identified a novel functional chimeric gene and also provided information regarding the molecular mechanisms regulating rice grain number.

Peanut (Arachis hypogaea L.) is a great plant protein source for human diet since it has high protein content in the kernel. Therefore, seed protein content (SPC) is considered a major agronomic and quality trait in peanut breeding. However, few genetic loci underlying SPC have been identified in peanuts, and the underlying regulatory mechanisms remain unknown, limiting the effectiveness of breeding for high-SPC peanut varieties. In this study, a major QTL (qSPCB10.1) controlling peanut SPC was identified within a 2.3 Mb interval in chromosome B10 by QTL-seq using a recombinant inbred line population derived from parental lines with high and low SPCs, respectively. Sequence comparison, transcriptomic analysis, and annotation analysis of the qSPCB10.1 locus were performed. Six differentially expressed genes with sequence variations between two parents were identified as candidate genes underlying qSPCB10.1. Further locus interaction analysis revealed that qSPCB10.1 could not affect the seed oil accumulation unless qOCA08.1_XH13 was present, a high seed oil content (SOC) allele for a major QTL underlying SOC. In summary, our study provides a basis for future investigation of the genetic basis of seed protein accumulation and facilitates marker-assisted selection for developing high-SPC peanut genotypes.

Introduction: Peanut (Arachis hypogaea L.) is an important cash crop worldwide. Compared with the ordinary peanut with pure pink testa, peanut with variegated testa color has attractive appearance and a higher market value. In addition, the variegated testa represents a distinct regulation pattern of anthocyanin accumulation in integument cells.Methods: In order to identify the genetic locus underlying variegated testa color in peanut, two populations were constructed from the crosses between Fuhua 8 (pure-pink testa) and Wucai (red on white variegated testa), Quanhonghua 1 (pure-red testa) and Wucai, respectively. Genetic analysis and bulked sergeant analysis sequencing were applied to detect and identify the genetic locus for variegated testa color. Marker-assisted selection was used to develop new variegated testa peanut lines.Results: As a result, all the seeds harvested from the F1 individuals of both populations showed the variegated testa type with white trace. Genetic analysis revealed that the pigmentation of colored region in red on white variegated testa was controlled by a previous reported gene AhRt1, while the formation of white region (un-pigmented region) in variegated testa was controlled by another single genetic locus. This locus, named as AhVt1 (Arachis hypogaea Variegated Testa 1), was preliminary mapped on chromosome 08 through bulked sergeant analysis sequencing. Using a secondary mapping population derived from the cross between Fuhua 8 and Wucai, AhVt1 was further mapped to a 1.89-Mb genomic interval by linkage analysis, and several potential genes associated with the uneven distribution of anthocyanin, such as MADS-box, MYB, and Chalcone synthase-like protein, were harbored in the region. Moreover, the molecular markers closely linked to the AhVt1 were developed, and the new variegated testa peanut lines were obtained with the help of marker-assisted selection.Conclusion: Our findings will accelerate the breeding program for developing new peanut varieties with “colorful” testa colors and laid a foundation for map-based cloning of gene responsible for variegated testa.