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Improvement of cold tolerance at the booting stage (CTB) in rice is a key strategy for cultivation in high-altitude and high-latitude regions. Here, we identify CTB3 gene, encoding a calmodulin-binding transcriptional activator that positively regulates cold tolerance at the booting stage in japonica rice. Two indels (57-bp and 284-bp) in the CTB3 promoter confer a differential transcriptional response to cold between the japonica and indica subspecies. OsTCP19 suppresses CTB3 expression by binding to these indels, negatively regulating cold tolerance. CTB3 activates the expression of TREHALOSE-6-PHOSPHATE PHOSPHATASE1 (OsTPP1), reducing trehalose 6-phosphate (Tre6P) levels, which increases sugar accumulation in panicles and improves cold tolerance. Additionally, favorable alleles of OsTCP19 and CTB3 are selected in japonica rice for cold adaptation. These findings highlight the important role of CTB3 in cold adaptation and its potential for improving cold tolerance in rice breeding. Cold tolerance at the booting stage is critical for the expansion of rice cultivation area. Here, the authors report that a CAMTA family transcription factor encoding gene CTB3 positively regulates japonica rice booting stage cold tolerance and its upstream and downstream interactors to fulfill the functionality. [ABSTRACT FROM AUTHOR] more...

Summary: Rice tillering is an important agronomic trait that influences plant architecture and ultimately affects yield. This can be genetically improved by mining favourable variations in genes associated with tillering. Based on a previous study on dynamic tiller number, we cloned the gene Tiller number 1a (Tn1a), which encodes a membrane‐localised protein containing the C2 domain that negatively regulates tillering in rice. A 272 bp insertion/deletion at 387 bp upstream of the start codon in the Tn1a promoter confers a differential transcriptional response and results in a change in tiller number. Moreover, the TCP family transcription factors Tb2 and TCP21 repress the Tn1a promoter activity by binding to the TCP recognition site within the 272 bp indel. In addition, we identified that Tn1a may affect the intracellular K+ content by interacting with a cation‐chloride cotransporter (OsCCC1), thereby affecting the expression of downstream tillering‐related genes. The Tn1a+272 bp allele, associated with high tillering, might have been preferably preserved in rice varieties in potassium‐poor regions during domestication. The discovery of Tn1a is of great significance for further elucidating the genetic basis of tillering characteristics in rice and provides a new and favourable allele for promoting the geographic adaptation of rice to soil potassium. [ABSTRACT FROM AUTHOR] more...

Summary: Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the "blue revolution" in agriculture. [ABSTRACT FROM AUTHOR] more...

SUMMARY: Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long‐term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra‐Geng subspecies remain largely unknown. Here, we identified MITOGEN‐ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome‐wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3Geng) directly evolved from Chinese Oryza rufipogon III and was largely retained in high‐latitude and high‐altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP‐776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9KL) promoter originated from novel variation of intra‐Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3Geng to colder climatic conditions in high‐latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3Geng and OsLEA9KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold‐adaptive differentiation of intra‐Geng, but also provides new genetic resources for rice molecular breeding in low‐temperature areas. Significance Statement: In this study, we identified variants in the two genes, OsMAPK3 and OsLEA9, as conferring cold tolerance of the Geng subspecies at the reproductive stage. OsMAPK3Geng originated from Chinese Oryza rufipogon III before following two evolutionary routes during domestication. It first genetically interacts with an allele of OsLEA9KL, which harbors a novel polymorphism in its promoter in Geng, to improve jointly the cold adaptability of Geng and promote its expansion to high‐altitude regions with a colder climate. In parallel, variation in OsMAPK3Geng sequentially move northward and enhance the tolerance of Geng to lower temperatures, eventually promoting the planting of Geng in higher‐latitude areas such as northeast China. Our results provide insights into the evolutionary path of cold tolerance genes underlying the cold adaptation of intra‐Geng and provide new genetic resources for rice molecular breeding for cold tolerance. [ABSTRACT FROM AUTHOR] more...