Genetic characterization of cucumber genetic resources in the NARO Genebank indicates their multiple dispersal trajectories to the East.

KEY MESSAGE: Genotyping-by-sequencing of 723 worldwide cucumber genetic resources revealed that cucumbers were dispersed eastward via at least three distinct routes, one to Southeast Asia and two from different directions to East Asia. The cucumber (Cucumis sativus) is an economically important vegetable crop cultivated and consumed worldwide. Despite its popularity, the manner in which cucumbers were dispersed from their origin in South Asia to the rest of the world, particularly to the east, remains a mystery due to the lack of written records. In this study, we performed genotyping-by-sequencing (GBS) on 723 worldwide cucumber accessions, mainly deposited in the Japanese National Agriculture and Food Research Organization (NARO) Genebank, to characterize their genetic diversity, relationships, and population structure. Analyses based on over 60,000 genome-wide single-nucleotide polymorphisms identified by GBS revealed clear genetic differentiation between Southeast and East Asian populations, suggesting that they reached their respective region independently, not progressively. A deeper investigation of the East Asian population identified two subpopulations with different fruit characteristics, supporting the traditional classification of East Asian cucumbers into two types thought to have been introduced by independent routes. Finally, we developed a core collection of 100 accessions representing at least 93.2% of the genetic diversity present in the entire collection. The genetic relationships and population structure, their associations with geographic distribution and phenotypic traits, and the core collection presented in this study are valuable resources for elucidating the dispersal history and promoting the efficient use and management of genetic resources for research and breeding in cucumber.

Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection.

Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset ("core collection") are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.

Theoretical investigation of CO2 capture in the MIL-88 series: effects of organic linker modification.

CO2 capture is a crucial strategy to mitigate global warming and protect a sustainable environment. Metal-organic frameworks with large surface area, high flexibility, and reversible adsorption and desorption of gases are good candidates for CO2 capture. Among the synthesized metal-organic frameworks, the MIL-88 series has attracted our attention due to their excellent stability. However, a systematic investigation of CO2 capture in the MIL-88 series with different organic linkers is not available. Therefore, we clarified the topic via two sections: (1) elucidate physical insights into the CO2@MIL-88 interaction by van der Waals-dispersion correction density functional theory calculations, and (2) quantitatively study the CO2 capture capacity by grand canonical Monte Carlo simulations. We found that the 1πg, 2σu/1πu, and 2σg peaks of the CO2 molecule and the C and O p orbitals of the MIL-88 series are the predominant contributors to the CO2@MIL-88 interaction. The MIL-88 series, i.e., MIL-88A, B, C, and D, has the same metal oxide node but different organic linkers: fumarate (MIL-88A), 1,4-benzene-dicarboxylate (MIL-88B), 2,6-naphthalene-dicarboxylate (MIL-88C), and 4,4'-biphenyl-dicarboxylate (MIL-88D). The results exhibited that fumarate should be the best replacement for both the gravimetric and volumetric CO2 uptakes. We also pointed out a proportional relationship between the capture capacities with electronic properties and other parameters.

Effects of functional groups in iron porphyrin on the mechanism and activity of oxygen reduction reaction.

The activity of the oxygen reduction reaction (ORR) on the cathode is one of the dominant factors in the performance of proton exchange membrane fuel cells. Iron porphyrin has low cost, environmental benignity, and maximum efficiency of metal usage. Therefore, this material can be a promising single-atomic metal dispersion catalyst for fuel cell cathodes. The variation of functional groups was proven to effectively modify the activity of the ORR on the iron porphyrin. However, the influences of functional groups on the mechanisms of the ORR remain ambiguous. This work paid attention to the substitution of carboxyl (-COOH), methyl (-CH3), and amino (-NH2) functional groups at the meso positions of the porphyrin ring. By using van der Waals density functional theory (vdW-DF) calculations, we found that the ORR mechanisms can follow the associative and dissociative pathways, respectively. The Gibbs free energy diagrams revealed that the rate-limiting step occurs at the second hydrogenation step for the first pathway and the O2 dissociation step for the second pathway for all considered functional groups. The thermodynamic energy barrier at the rate-limiting step was found to be in the following order: porphyrin-(CH3)4 < porphyrin-(NH2)4 < original porphyrin < porphyrin-(COOH)4 for the associative mechanism and porphyrin-(NH2)4 < porphyrin-(CH3)4 < porphyrin-(COOH)4 < original porphyrin for the dissociative pathway. The findings suggested that porphyrin-(CH3)4 and porphyrin-(NH2)4 should be the best choices among the considered substrates for the oxygen reduction reaction. Furthermore, the interaction between the ORR intermediates and the substrates was attributed to the resonance of the d z 2 , d xz , and d yz components of the Fe d orbital and the C and N p orbitals of the substrates with the p orbitals of the oxygen atoms in the intermediates. Finally, the nature of the interaction between the adsorbent and adsorbate was charge transfer.

Distribution of two groups of melon landraces and inter-group hybridization enhanced genetic diversity in Vietnam.

To understand the genetic diversity and differentiation of Vietnamese melon (Cucumis melo L.), we collected 64 landraces from the central and southern parts of the country and assessed molecular polymorphism using simple sequence repeat and random amplified polymorphic DNA markers. The Vietnamese melon was divided into seven cultivar groups, namely "Dua le", "Dua vang", "Dua bo", "Dua gang-andromonoecious", "Dua gang-monoecious", "Dua thom", "Montok", and the weedy-type melon "Dua dai". Among these, Dua le, Dua vang, Dua bo, and Dua gang-andromonoecious are cultivated on plains and they formed cluster II along with the reference accessions of Conomon and Makuwa. Based on genetic distance, Dua le and Dua vang were regarded as Makuwa and Dua bo and Dua gang-andromonoecious as Conomon. In contrast, Dua thom and Montok are cultivated in highlands, and they formed cluster III along with landraces from the southern and eastern foot of the Himalayas. Dua gang-monoecious which is commonly cultivated in the southern parts of Vietnam, exhibited the greatest genetic diversity, as explained by its possible origin through the hybridization between Dua gang-andromonoecious and Montok. Genetic differences in melon landraces between plains and highlands and hybridization between these two geographical groups have contributed to the enhancement of genetic diversity in Vietnamese melon.