Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field

Abstract

Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.

Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China’s Deserts Based on the Resequencing of the Genome

“…The technology of resequencing sequencing contributes significantly to the investigation of the genetic information of a vast array of species, particularly non-model organisms [5][6][7][8]. Through flow karyotyping, which detects alterations in chromosome number and structure, we analyzed chromosomal polymorphisms [83,84].…”

“…Differential selection pressures caused by the spatial heterogeneity of the environment on natural populations may cause a species to adapt variably throughout its range [3,4]. While microevolutionary investigations pertaining to this subject are not uncommon, they are frequently carried out on model plants and cash commodities [5][6][7][8]. A growing number of interests has been focused on the environmental adaptability benefits of genomic population genetics research [9].…”