Ya-Ping Lin

Amaranthus tricolor is a climate-resilient orphan crop whose betalain pigments contribute to nutritional quality and stress tolerance. However, breeding efforts have traditionally relied on field yield trials due to the limited availability of genomic information and genetic resources. To address this gap, we first used the Illumina and PacBio sequencing platforms to assemble a novel reference genome of A. tricolor , using the Japanese cultivar Bayam. By combining this reference genome with a core collection developed in our previous study, we aimed to identify genomic regions associated with pigmentation-related traits across winter and summer seasonal environments. Betalains are antioxidant phytonutrients that contribute to abiotic stress tolerance, making the regulation of their biosynthesis under heat stress particularly relevant for developing climate-resilient crops such as A. tricolor. As a result, ATR1.0CH03_5131103, which is associated with ATR1.0ch03g000565, was identified under the winter seasonal environment. Meanwhile, transcriptomic profiles in this study revealed that ATR1.0ch03g000565 was differentially expressed under both control and heat stress conditions, suggesting that it may be associated with the regulation of CYP76AD1 expression under optimal conditions. Under the elevated-temperature treatment, transcript levels of CYP76AD1 and 5GT decreased in Am087, coinciding with lower betacyanin_dominated absorbance indices. cDOPA -like homologs were upregulated; however, pigmentation-related absorbance remained reduced. Further molecular experiments, such as CRISPR-Cas9 knockouts or overexpression studies, are necessary to validate the regulatory mechanisms of CYP76AD1 and 5GT under heat stress.

Mungbean [ Vigna radiata (L.) Wilczek], an important leguminous crop, is grown on more than six million hectares worldwide. However, mungbean is very susceptible to the common leaf‐feeding cutworm ( Spodoptera litura ), and its defence mechanism against S. litura is not fully understood. By integrating an ‘omic’ approach and comparing the results between the resistant wild accession (CQ3112) and susceptible cultivar (Crystal) after S. litura attacks, this study identified the key defensive regulatory genes and bioactive metabolites involved in resistance to S. litura . The transcriptomic results demonstrated that VrMYC2 , VrAOC , VrGH3 and VrPPO are involved in defence responses associated with jasmonic acid (JA) signalling, and VrUGT84A24 , VrIOMT and VrEBOS , involved in the terpenoid and flavonoid biosynthesis, are up‐regulated in responses to S. litura attacks. The metabolomic results further confirmed that JA, glucosylated kaempferol and ( E )‐β‐ocimene are accumulated in CQ3112 accession, supporting defence response to S. litura infestation. Moreover, feeding S. litura larvae with kaempferol‐7‐O‐glucoside (K7G), a non‐volatile metabolite identified in this study, showed S. litura growth and mortality reductions. Taken together, this study provides solid evidence that K7G functions as an insecticidal compound to control S. litura attacks. Also, the genes involved in defence against S. litura could provide genetic information for the improvement of mungbean breeding programmes.

Tomato ( Solanum lycopersicum L.) production is severely impacted by biotic stresses, leading to significant yield losses. Developing genetically resistant cultivars presents a sustainable alternative to chemical control, which is often costly and ineffective against evolving pathogens. This study utilized molecular markers to assess genetic resistance to key tomato diseases, including Fusarium wilt, late blight, bacterial wilt, root-knot nematode, Tomato Mosaic Virus (ToMV), and Tomato Yellow Leaf Curl Virus (TYLCV), across 964 tomato accessions comprising both wild germplasm and cultivated varieties. Wild germplasm exhibited the highest frequencies, with S. peruvianum identified as a rich reservoir of resistance loci. Markers associated with TYLCV ( Ty-1/3, Ty2 ) and Fusarium wilt (I2(OH)) were particularly prevalent in wild species. The potential for gene pyramiding potential was evident, with some wild accessions carrying up to six resistance loci. In contrast, resistance loci were limited in Solanum lycopersicum . Two S. lycopersicum germplasm collections were screened: a geographically representative collection from four Southeast Asian national genebanks and a genetically representative core collection from global public genebanks. The highest resistance frequencies in S. lycopersicum were observed for bacterial wilt-associated markers SLM12-2 and SLM12-10. However, the overall scarcity of resistance alleles in S. lycopersicum emphasizes the need for further introgression of resistance genes from wild relatives. This study provides valuable genetic insights into tomato germplasm for combating biotic stress, forming a foundation for sustainable breeding strategies to enhance disease resistance and safeguard global tomato production.

Orphan crops are considered essential climatic-resilient genetic resources due to their native adaptability to various ecological environments. Amaranthus tricolor is one of a few common vegetables widely cultivated in tropical and subtropical regions. Strong vigor, abiotic-stress adaptability, and nutrition richness make it an ideal vegetable to provide food and nutrient security for smallholders. However, the breeding efforts depend on the field yield trials because little genomic information or genetic resources can be accessed. To fill this gap, we first used the Illumina and Pacbio sequencing systems to assemble a novel reference genome of A. tricolor using a Japanese variety Bayam. Together with a core collection developed in our previous study, we investigated the genetic mechanism of betalain biosynthesis under optimal and heat-stress conditions. Betalain is an antioxidant phytonutrient commonly appearing in beets and amaranths. As a result, ATR1.0CH03_5131103 which associate with ATR1.0ch03g000565 was identified in the optimal condition. Meanwhile, according to the transcriptomic profiles in this study, ATR1.0ch03g000565 also show significantly differential expressions under control and heat stress conditions, suggesting this candidate gene regulates the optimal performance of CYP76AD1 . Meanwhile, among the homologous genes involving in the betalain biosynthesis, CYP76AD1 and 5GT were down-regulated under heat stress conditions; cDOPA was up-regulated. This result suggested heat stress reduces betacyanin biosynthesis through the downregulation of CYP76AD1 and 5GT ; despite that the upregulation of cDOPA cannot rescue the decrease of betalain. More molecular experiments are required to address the regulation of these three enzymes.

Background: High temperature severely limits tomato reproductive development and yield, particularly in tropical production systems. Pollen viability and fruit set are commonly used as indicators of reproductive heat tolerance, but much of the supporting evidence has been obtained under controlled conditions. Their relevance to breeding under variable open-field environments remains less clear. This study investigated reproductive performance and its genetic basis under open-field heat stress using a multi-parent advanced generation inter-cross (MAGIC) population. Results: We developed a MAGIC population from eight Solanum lycopersicum parents combining heat tolerance and multiple disease resistances and evaluated 262 F _5:6 lines under natural open-field heat stress. Flower number showed the highest heritability (0.64), followed by pollen viability (0.56), fruit number (0.48), and days to flowering (0.25), whereas fruit set showed negligible heritability (r = 0.22). In contrast, fruit number was strongly correlated with fruit set ( r = 0.86), supporting fruit number as a practical selection criterion for reproductive performance under open-field heat stress. Restriction enzyme-associated DNA sequencing generated 16,350 high-quality SNPs for genome-wide association analysis, which identified multiple QTLs for reproductive traits, several overlapping previously reported loci. A region on chromosome 6 at approximately 31–33 Mb was particularly notable because it was associated with multiple reproductive traits and coincided with a previously reported heat-responsive QTL region. Candidate-gene analysis highlighted floral developmental regulation, represented by positional candidates SlAGO7 , ENO , and SlWUS , and cellular and protein homeostasis, supported by direct candidates including MON1, ECM29, and ubiquitin-related genes. Conclusions: Selection criteria established under controlled environments may not fully predict reproductive performance under open-field heat stress. Fruit number provides an integrative and moderately heritable indicator of realized reproductive success under field conditions. The identified QTLs and candidate genes provide targets for validation and development of heat-tolerant tomatoes adapted to tropical open-field production.

Grown on 7 million ha, mungbean is a warm‐season grain legume with regional importance in parts of Asia and Africa. Under forecasted climate change, due to its tolerance to drought and heat, the short crop duration, and its nutritional properties, mungbean could serve to fill an important need for human diets. However, selection of accessions becomes difficult where plant and consumer market variation is large. We performed selection on genebank accessions, specifically the mini‐core collection at the World Vegetable Center, for yield and yield component traits. Our selection index uses refined accuracy by leveraging genomics, phenomics, and genotype‐by‐environment interactions. Best linear unbiased prediction (BLUP) is used to predict the genotypic effects of the 292 mini‐core accessions toward seed yield based on genomic relationships formed from ∼200,000 SNPs. We expanded BLUP analysis to predict phenotypic effects based on the phenomic relationships formed from ∼75,000 measurements from three‐dimensional multispectral data. While this method is restricted to a single environment, our multi‐environment trials across eight countries and 4 years serve to quantify the genotype‐by‐environment effect. K‐fold cross‐validation finds predictive ability to vary by methods but to be related to the narrow‐sense heritability of the yield component trait. Our weighted rank sum index (WRSI) linearly combines yield component traits to proxy yield within our single environment phenomics trial by first ranking genomic and/or phenomic BLUPs, then weighting by predictive accuracy from the cross‐validated model, and then summing the component weighted ranks for each accession. Selections were made from the predicted random effects in each location, identifying three accessions overlapping across both methodologies: PI 369787 (VI001339A‐G) and EG‐MD‐6D (VI000380A‐G) from the Philippines, and PI 363534 (VI003220A‐G) from India.

Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome re-sequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying two key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago (kga). Later in Asia, the cultivated form diverged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found two ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of two important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.