An insight into the morphological, biochemical and molecular diversity of GI tagged black scented rice, <i>Chakhao</i> landraces of Manipur, India

Abstract The northeast region of India, part of the Indo–Burma biodiversity hotspot, is a vital reservoir of genetic diversity for agricultural crops, particularly rice. Chakhao , the black scented rice of Manipur, India is celebrated for its mild nutty flavour, distinctive aroma and high anthocyanin content. This study evaluated 22 economically significant Chakhao landraces using DUS characterization, along with biochemical and molecular profiling. Key findings revealed low amylose content (3.4–6.97%) and diverse grain types, predominantly short to medium slender. Anthocyanin concentrations varied widely, with certain genotypes surpassing 350 mg/100 g – levels even higher than those found in blueberries. Notably, landraces such as Chakhao_Bn-4, Chakhao_Ch-2, Chakhao_Cp-1 and Chakhao_IE-1 exhibited exceptional anthocyanin content (&gt;390 mg/100 g), making them excellent candidates for future breeding programs. These lines also score the highest (9 – dark purple) in decorticated grains colour, a key trait for geographical indication (GI) status. Anthocyanin-related traits such as were the primary contributors to phenotypic diversity in the first three principal components, while structural and developmental traits influenced subsequent components. The study also revealed a striking lack of similarity in groupings based on morphological versus molecular data, as indicated by a low Baker’s Gamma correlation coefficient (0.034). Multivariate analysis integrating both data types highlighted substantial genetic and phenotypic diversity, reinforcing the necessity for comprehensive conservation strategies. The recent GI status of Chakhao has boosted global interest in Chakhao , prompting an initiate crop improvement program utilizing these landraces to drive economic resilience in marginal farming communities.