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Summary Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high‐quality chromosome‐level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long‐read sequencing with short‐read and Hi‐C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein‐coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole‐genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome‐wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.

The present paper deals with the report on the potential of Vigna angularis var. nipponensis (Ohwi) Ohwi and H. Ohashi assembled from Northeastern hill region (NEH) of India. The total of four exploration missions were conducted in remote and highaltitude areas of Nagaland, Arunachal Pradesh and Mizoram during 2011, 2016, 2017 and 2019 to confirm the occurrence, localities of new distribution and genetic resource study. Preliminary studies on seed germination and morpho-nutritional evaluation of seed of both cultivated and wild forms were also conducted. Conserving precious germplasm of this less represented wild relative of adzuki bean { Vigna angularis (Willd.) Ohwi and Ohashi} assumes great significance for its use in breeding and improvement of Vigna crop group.

Genetic differences between azuki bean (Vigna angularis var. angularis) and its presumed wild ancestor (V. angularis var. nipponensis) were resolved into QTL for traits associated with adaptation to their respective distinct habits. A genetic linkage map constructed using progenies from a cross between Japanese cultivated and wild azuki beans covers 92.8% of the standard azuki bean linkage map. A reciprocal translocation between cultivated and wild azuki bean parents was identified on the basis of the linkage map having a pseudolinkage group and clustering of seed productivity-related QTL with large effect near the presumed breakpoints. In total, 162 QTL were identified for 46 domestication-related traits. Domestication of azuki bean has involved a trade-off between seed number and seed size: fewer but longer pods and fewer but larger seeds on plants with shorter stature in cultivated azuki bean being at the expense of overall seed yield. Genes found related to germination and flowering time in cultivated azuki bean may confer a selective advantage to the hybrid derivatives under some ecological conditions and may explain why azuki bean has evolved as a crop complex in Japan.

Recent archaeological findings provide a hint on domestication of azuki (Vigna angularis var. angularis) in East Asia. This preliminary study investigates archaeological collections from various regions in Korea, China, and Japan, representing the long-term evolution (5300–1450 BP) of azuki. Changes in seed shapes show that cultural manipulation of azuki began as early as 5300–4800 cal. BP. Azuki beans from Neolithic contexts in Korea and Japan show a possible sign of morphological response to human management, at least 2000 years prior to the appearance of fully domesticated forms. Yabutsuru-azuki (V. angularis var. nipponensis), a conspecific progenitor of domesticated azuki, has been a supplementary diet and seed reserve for lean years in East Asia, and this tradition may have a long root to the mid Holocene. Archaeological evidence indicates the possibility of multiple origins of azuki, supporting recent phylogenetic data. A unique contribution of this research is its interdisciplinary attempt to examine both the biological and cultural processes of this staple legume domestication.

To gain a better understanding of wild and weedy azuki population structures in relation to the cultigens we have developed simple sequence repeat (SSR) markers based on a new methodology for plant material. In the azuki bean genome, the number of (AG)n and (AC)n motif loci per haploid genome has been estimated to be 3,500 and 2,100, respectively, indicating that (AG)n motifs are a rich source of markers. We constructed a (AG)n-SSR-enriched library in azuki bean in order to obtain a comprehensive range of SSR markers efficiently. The method applied in this study resulted in a 116-fold enrichment over the non-enriched genomic library, with a high percentage (98%) of successful single-locus amplification by the primer pairs designed. Consequently, this method can be applied to construct SSR-enriched libraries suitable for large-scale sequencing. We obtained 255 unique sequences from an (AG)n-enriched library for azuki bean. Fifty primer pairs were designed and screened against five populations of wild azuki bean. Among these five populations, one population from Bato town, Tochigi prefecture, Japan, showed greater polymorphism using these primers than the others and was therefore chosen for the in-depth study. The genotypes of 20 individuals were investigated using eight of the SSR primers developed. The genetic relationships among individuals revealed a complex spatial pattern of population structure. Although azuki bean is considered to be a predominantly self-pollinating species, 3 of the 20 individuals tested in the population showed heterozygous genotypes, indicating outcrossing. Allele size and DNA sequence in each of the 20 individuals were compared with those of landraces and released cultivars of azuki bean. Plants in part of the population had many alleles of the same size and with the same sequence as those in cultivated azuki bean, suggesting that gene flow from the cultigen to wild plants has occurred in this population. Unintentional transgene escape from azuki could therefore occur when transgenic azuki is grown in areas where its wild and weedy relatives occur. The approach used here could be applied to biosafety monitoring of transgenic azuki bean.

Wild azuki bean, a progenitor of an Asiatic food legume (Vigna angularis var. nipponensis: Fabaceae), and its weed form are distributed widely in the Japanese Archipelago. The straggling or climbing wild form occurs in sleeve or mantle plant communities, and the weakly climbing or bushy weed form is found in relatively open human-disturbed habitats. The wild form has small seeds with a black-mottled pattern on green or grey skin; the weed form has larger seeds with variable color patterns. Wild and weed forms have black, easily dehiscent pods, distinct from their cultivated counterpart which has red large seeds and indehiscent light-colored pods. The wild form is not utilized, but the weed form is recognized by farmers and has several folk names as a weed, a contaminated form of azuki bean, and a substitute for azuki as a food. The frequent occurrence of weed azuki bean in Japan is attributable to adaptation of the wild form to lack of climbing support in human-disturbed habitats, escape from old cultivars, and natural establishment from the derivatives of hybrids between cultivars and wild forms. / Die Wildazukibohne, ein Vorfahr einer asiatische Eßbarbohne (Vigna angularis var. nipponensis: Fabaceae), und dieser Unkrautform sind weitverbreit in der japanischen Inselgruppe. Die üppigwachende oder aufsteigende Wildform liegt in den Saum- oder Mantelpflanzengesellshaften, und die schwächliche aufsteigende oder buschige Unkrautform wird in den relativoffen menschenausstörend Standorten gefunden. Die Wildform trage die kleinen Samen mit einem schwarzgefleckten Muster auf der grauen oder grünen Samenhaut; die Unkrautform trage die größeren Samen mit dem variabelen Färbung und Zeichnung. Wild- und Unkrautformen haben die schwarzen und lechtspaltigen Hülsen, distinktem vom ihnen Kulturgegenstück, der hat die roten großen Samen und die inspaltigen hellfarben Hülsen. Die Wildform wird nicht gebenutzen, aber die Unkrautform wird angeerkennen bei den Bauern und hat fieln Volksnamen als einen Unkrauten, einen Befleckungformen der Azukibohne, und zum Ersatz für Azuki zu Eßzwecken. Das häufige Dasein der Unkrautazukibohne in Japan ist der Anpassung der Wildform zu Mangel der aufsteigenden Stüze in den menschenaussörenden Standorten, dem Verwilderung von alten Kulturvarietäten, und der natürlichen Gründung von der Ableitung der Hybriden zwischen Kulturvarietäten und Wildformen hervorgekommen.