Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporter genes, namely, NcHMA3, NcHMA4, and NcIREG2, are consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in the roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participates in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of several metal transporters, including NcIREG2, and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.

Durio zibethinus Murr., commonly known as durian or the “King of Fruits,” is prized for its strong aroma, spiny rind, and unique flavor. With global demand rising, it has become a key export, especially for Thailand, which led the market in 2024 with US$4.4 billion in revenue. However, breeding efforts are hindered by limited genetic diversity research, long generation times, and environmental sensitivity. These challenges are compounded by weak enforcement of intellectual property protections under Thailand’s Plant Variety Protection Act (PVP), which limits incentives for breeders. To address this, Thailand has turned to Geographical Indications (GIs) to protect and promote region-specific varieties. By 2024, 17 GI designations were granted across 16 provinces, including the notable Monthong durian from Pakchong in Nakhon Ratchasima. Although classified under the Monthong group, genetic similarity was observed, while notable phenotypic variation exists among varieties. These differences may be attributed to specific agronomic or genetic traits, warranting investigation into the cultivation characteristics that influence consumer-related qualities and preferences. Strengthening supply chain standards through good agricultural practices, GIs, genetic profiling, and international certification, combined with the adoption of modern molecular breeding tools including marker-assisted selection, genomic selection, and CRISPR/Cas9, would support sustainable innovation, improved farmer revenues, and long-term global competitiveness in the durian industry across Southeast Asia.

Noccaea caerulescens is a metal hyperaccumulator plant species with the capacity to accumulate high concentrations of zinc (Zn), cadmium (Cd) and nickel (Ni). Several candidate genes have so far been associated with accumulation and tolerance of these metals, but gene function analysis has been cumbersome in the absence of an efficient stable plant transformation method for N. caerulescens. A previously identified mutation in the FLOWERING LOCUS C gene, conferring early flowering to the calamine accession St. Felix de Pallières, has been introgressed in the genetic background of five different genotypes, originating from the calamine populations Clough Wood (CLW) and Le Blémard (BLE), the ultramafic population Cira (CIR), and the non-metallicolous populations St. Baudille (SBD) and Werschmatt (WER). Agrobacterium tumefaciens mediated floral dipping transformation was employed in five introgression lines in these backgrounds and in Arabidopsis thaliana as control. Three introgression lines, of genetic backgrounds CLW, BLE and SBD, were successfully transformed, achieving an average transformation efficiency ≥ 0.29% for each background. A reproducible, stable transformation method based on floral dipping is presented here as an improvement on previously reported methods. The early flowering N. caerulescens flc mutation can be readily introgressed into different genetic backgrounds to facilitate genetic transformation studies, which is expected to provide a highly desired extra genetic tool to study gene function analysis in the metal hyperaccumulator N. caerulescens.

Durio zibethinus Murr., commonly known as durian or the "King of Fruits," is prized for its strong aroma, spiny rind, and unique flavor. With global demand rising, it has become a key export, especially for Thailand, which led the market in 2024 with US$4.4 billion in revenue. However, breeding efforts are hindered by limited genetic diversity research, long generation times, and environmental sensitivity. These challenges are compounded by weak enforcement of intellectual property protections under Thailand’s Plant Variety Protection Act (PVP), which limits incentives for breeders. To address this, Thailand has turned to Geographical Indications (GIs) to protect and promote region-specific varieties. By 2024, 17 GI designations were granted across 16 provinces, including the notable Monthong durian from Pakchong in Nakhon Ratchasima. Although classified under the Monthong group, genetic similarity was observed, while notable phenotypic variation exists among varieties. These differences may be attributed to specific agronomic or genetic traits, warranting investigation into the cultivation characteristics that influence consumer-related qualities and preferences. Strengthening supply chain standards through good agricultural practices, GIs, genetic profiling, and international certification would support sustainable economic growth, improved farmer revenues, and long-term global competitiveness in the durian industry.

Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum, to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporters, namely NcHMA3, NcHMA4 and NcIREG2, is consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participate in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of few metal transporters including NcIREG2 and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.