The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, 3, 3, and 3 EXLAs, alongside 11, 9, 13, and 8 EXLBs, in diploid I. trifida strain Y22, wild tetraploid I. batatas strain Y428B, and hexaploid I. batatas strain Y601, and cultivated sweet potato ‘Nancy Hall’, respectively. A comprehensive bioinformatic analysis of the expansin-like genes and proteins was performed to reveal their potential roles in SR development. Gene expression profiling showed that EXLA members were expressed during SR development, while approximately half of the EXLB members were expressed in Y22, Y428B (pencil root), Y601, and NH, respectively. Proteomic analysis (4D-DIA) detected 2, 1, 1, and 1 EXLAs, and 3, 3, 3, and 3 EXLBs in the mature SRs of the respective species. Integrated transcriptomic and proteomic analyses suggested that downregulating Iba6xEXLB2 and Iba6xEXLB1 may be associated with SR swelling in sweet potato. Furthermore, subcellular localization assays confirmed that Iba6xEXLB2 and Iba6xEXLB8 are localized to the cell wall/membrane. This study enhances the understanding of the expansin-like gene subfamily in sweet potato and its wild relatives and lays the groundwork for future functional studies on the role of expansin-like genes in SR development.

This study aimed to explore the genetic information about the yield traits in perennial Chinese rice "Shendao3^#" and provide a series of theoretical bases for the innovative utilization of perennial Chinese rice germplasm. The F₂ population derived from the cross between perennial Chinese rice "Shendao3^#" and one annual rice "XiqingzaoB" was developed to identify QTLs’ underlying yield-related traits. Fifteen yield traits including plant height, panicle plant^-1, and thousand-grain weight were measured for the QTL mapping. The software packages Excel 2010, GraphpadPrism 5.0, and QTLIciMapping 4.10 were used to perform the phenotypic data analysis, construction of molecular map, and QTL mapping, respectively. Results indicated 15 yield-related traits displaying normal distribution and belonging to quantitative trait inheritance. A total of 25 QTLs associated with the yield-related traits and 26 epistatic QTLs were detected on the whole genome except for the 6th and 12th chromosomes. This finding explained phenotypic variance with ranging from 4.21% to 27.30% and 1.15% to 19.30%, respectively. Six pleiotropic QTL (chromosomal regions) underlying two or more yield-related traits were detected on the 1st , 4th, 7th, 8th, and 11th chromosomes, respectively. Among 25 QTLs underlying a single yield-related trait, 11 were primarily identified in the perennial Chinese rice "Shendao3^#". All QTLs underlying 15 yield-related traits followed the genetic model of additive, dominant, and digenic epistatic of additive by additive, additive by dominant, dominant by additive, and dominant by dominant. This work can serve as a good foundation for yield-related gene mining and its utilization in breeding the perennial Chinese rice "Shendao3^#".

Shendao3^# (SD3^#) exhibits perennial characteristics. Identifying the QTLs underlying the yield-related traits in SD3^# provides a theoretical basis for future perennial rice breeding. In this study, SD3^# and an F₂ population derived from a cross between SD3^# and XieqingzaoB (XQZB) and its bi-parents were selected as experimental materials. A total of fifteen yield-related traits including plant height, effective panicle per plant and thousand-grain weight in the SD3^#-population and its bi-parents were investigated for both phenotypic analysis and QTL mapping. Results indicated that the fifteen yield-related traits in the SD3^#-population exhibited quantitative genetic characteristics suitable for QTL analysis. Altogether, 25 QTLs underlying the yield-related traits and 26 pairs of epistatic QTLs were identified; these explained phenotypic variances ranging from 4.21% to 27.30% and 1.24% to 19.30%. Of these, nine novel QTLs underlying unfilled grain per panicle (UGP), spikelet per panicle (SP), seed setting density (SSD), grain yield per plant (GYP) and thousand-grain weight (TGW) with additive effects derived from SD3^# were detected on the first, second, fourth, eighth, ninth, and tenth chromosomes. Six pleiotropic QTLs underlying two or more traits were detected on the first, fourth, seventh, eighth, and eleventh chromosomes. This work lays a good foundation for both the yield-related gene mined from SD3^# and future perennial Chinese rice breeding.

NAC transcription factors are plant-specific regulators involved in growth, development, and stress responses, but their roles in sweetpotato storage root (SR) enlargement remain largely unknown. In this work, we identified 134, 142, 132, and 126 NAC members in diploid Ipomoea trifida Y22, wild tetraploid I. batatas Y428B, wild hexaploid I. batatas Y601, and cultivated sweetpotato 'Nancy Hall' (NH), respectively, and classified them into 19 subfamilies. These genes are unevenly distributed across 15 chromosomes of their respective genomes. We conducted a comprehensive analysis of their physical and chemical properties, as well as the structures of their genes and proteins. The collinearity analysis revealed that among all NAC genes, we identified 292 pairs of genes that were highly correlated. Gene expression profiling showed that in SR-forming species (Y22, Y601, and NH), many NAC genes are progressively upregulated during SR development, whereas in pencil root (Y428B), most NAC genes exhibit high expression in adventitious roots that sharply declines thereafter, with few showing the gradual upregulation observed in swelling types. Proteomic analysis (4D-DIA) detected 3–5 NAC proteins at the mature SR stage, further supporting the transcript-protein decoupling. The high expression of Iba4xNAC028 may promote pencil root formation in Y428B, while the high expression of Ibw6xNAC022 and Itr2xNAC069 may be unfavorable for SR swelling. Promoter cis-element analysis of the 15 protein-detected NAC genes indicated enrichment of ABA-, MeJA-, and GA-responsive elements, with ABA and MeJA being the most prevalent, implying their involvement in SR enlargement and stress responses via hormone signaling cross-talk. This study enhances our understanding of the expression regulation of the NAC family in sweetpotato and its wild relatives, and provides candidate genes for future functional validation and molecular breeding.