Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China

Amid the rapid increase of the global population and the quest for sustainable agriculture, the need for enhanced rice breeding strategies has become increasingly pronounced, particularly in Heilongjiang, China's foremost rice-producing province, renowned for its premium temperate <i>japonica</i> rice. Here, we conducted an extensive genomic investigation of the elite rice cultivars developed in Heilongjiang Province. Using whole-genome re-sequencing of a total of 376 representative cultivars from Heilongjiang, of which 14 were developed by a single research group, we identified 4.9 million single nucleotide polymorphisms (SNPs) and 0.98 million insertions and deletions (InDels), offering a comprehensive perspective on genetic diversity and population structure. We classified the 376 rice cultivars into five subgroups based on their breeding years. Recently bred cultivars, assigned to subgroups HLJ-IV-1 and HLJ-IV-2, showed notable genetic differentiation. Through a selective sweep analysis, significant genomic variation in genes such as <i>OsACBP5</i>, <i>Os4CL5</i>, and <i>GFR1</i> was pinpointed, reflecting a concerted effort in selecting for broad-spectrum disease resistance and enhanced tillering capacity. Furthermore, to identify the strengths and areas for improvement within those series, we conducted an exhaustive analysis of aromatic compounds and their corresponding genes <i>OsODC</i> and <i>OsBadh2</i>, as well as the advantageous long-grain gene <i>OsGL3.1</i> haplotype within Hagengdao7. Additionally, strategies for reducing plant height through the introduction of the <i>sd1</i> gene have been elucidated. With a commitment to expediting the development of superior rice cultivars, our discoveries are poised to raise the sensory attributes and nutritional profile of rice, thereby bolstering the resilience and sustainability of global food systems.