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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]

Drought is a major environmental stress limiting crop yields worldwide. Upland rice (Oryza sativa) has evolved complex genetic mechanisms for adaptative growth under drought stress. However, few genetic variants that mediate drought resistance in upland rice have been identified, and little is known about the evolution of this trait during rice domestication. In this study, using a genome-wide association study we identified ROOT LENGTH 1 (RoLe1) that controls rice root length and drought resistance. We found that a G-to-T polymorphism in the RoLe1 promoter causes increased binding of the transcription factor OsNAC41 and thereby enhanced expression of RoLe1. We further showed that RoLe1 interacts with OsAGAP, an ARF-GTPase activating protein involved in auxin-dependent root development, and interferes with its function to modulate root development. Interestingly, RoLe1 could enhance crop yield by increasing the seed-setting rate under moderate drought conditions. Genomic evolutionary analysis revealed that a newly arisen favorable allelic variant, proRoLe1 −526T, originated from the midwest Asia and was retained in upland rice during domestication. Collectively, our study identifies an OsNAC41-RoLe1-OsAGAP module that promotes upland rice root development and drought resistance, providing promising genetic targets for molecular breeding of drought-resistant rice varieties. A genome-wide association study identified a root length and drought resistance-related gene RoLe1 , which is directly activated by OsNAC41. RoLe1 interacts with OsAGAP and decreases its abundance, leading to a reduced influx rate of IAA in rice roots. Introducing a favorable RoLe1 haplotype into drought-sensitive rice varieties significantly enhances drought resistance. [ABSTRACT FROM AUTHOR]

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]

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]

BACKGROUND: High‐molecular‐weight glutenin subunits (HMW‐GSs) have important effects on bread‐making quality. Allelic variations of HMW‐GS in bread wheat varieties contribute in different ways to dough properties and bread volume. However, no systematic analysis has been done on the effects of allelic variation on bread‐crumb structure, an important parameter when evaluating bread‐making quality. In this study, seven Glu‐1 deletion lines and one intact line harboring different encoding loci and derived from a cross between two spring wheat cultivars were used to investigate the contribution of a single Glu‐1 locus, or combination of Glu‐1 loci, to the crumb structure. RESULTS: Deletion of HMW‐GS locus combinations resulted in a decline in slice size, brightness, and fineness of the bread crumb. A desirable crumb structure correlated well with preferred subunit combinations: high levels of GMPs, superior dough properties, and loaf volume. The effects of the HMW‐GS combinations were ranked as Dx5 + Dy10 > Bx17 + By18 > Ax1 + Null. The Ax1 + Null allele affected the crumb structure by interacting with the Bx17 + By18 or Dx5 + Dy10. CONCLUSION: High‐molecular‐weight glutenin subunits had significant effects on the loaf volume and crumb structure; varying effects from different subunit combinations were observed. © 2018 Society of Chemical Industry [ABSTRACT FROM AUTHOR]