Rice Domestication Research Articles

Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs.

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.

The genetic control of long sterile lemma during African rice domestication

The genetic control of long sterile lemma during African rice domestication

COLD6-OSM1 module senses chilling for cold tolerance via 2′,3′-cAMP signaling in rice

While it is known that temperature sensors trigger calcium (Ca2+) signaling to confer cold tolerance in cells, less is known about sensors that couple with other secondary messengers. Here, we identify a cold sensor complex of CHILLING-TOLERANCE DIVERGENCE 6 (COLD6) and osmotin-like 1 (OSM1), which triggers 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) production to enhance cold tolerance in rice. COLD6, which is encoded by a major quantitative trait locus (QTL) gene, interacts with the rice G protein α subunit (RGA1) at the plasma membrane under normal conditions. Upon exposure to chilling, cold-induced OSM1 binds to COLD6, kicking out RGA1 from interaction. This triggers an elevation of 2',3'-cAMP levels for enhancing chilling tolerance. Genetic data show that COLD6 negatively regulates cold tolerance and functionally depends on OSM1 in chilling stress. COLD6 alleles were selected during rice domestication. Knockout and natural variation of COLD6 in hybrid rice enhanced chilling tolerance, hinting design potential for breeding. This highlighted a module triggering 2',3'-cAMP to improve chilling tolerance in crops.

Rice and its nutritional significance

Rice is a staple food for millions of populations in the world and originated from a wild grass to a crop. The Asian civilization was built on rice. The rice cultivation changed the lives of hunters into farmers. The domestication of rice in India dates back to the 7th millennium BC. Due to industrialization, the traditional practice of hand pounding was overtaken by rice processing mills, which led to the production of white polished rice, devoid of many nutrients. Studies confirmed that higher consumption of white rice increased the risk for diabetes and cardiovascular disease, high in India. In the current scenario, the disease prevalence is increasing, and customers are in search of nutritious foods with potential health benefits. This paper outlines the origin of rice and its nutritional value.

How Does Cultural and Colonial Heritage Affect Optimal Branding Strategies? Evidence From the Rice Sector in Senegal

ABSTRACTAfrica's cultural and colonial heritage has profoundly segmented rice markets. Whereas in ancient centers of rice domestication, consumers maintained preferences for local rice consistent with their cultural heritage, preferences have shifted toward imported Asian rice in coastal areas around seaports, due to prior exposure to colonial import substitution policies. To enhance the competitiveness of locally produced rice relative to imported versions, it is necessary to tailor new local rice products to both market segments. A study was conducted in Senegal to test branding strategies for local rice in a country where both market segments coexist. Brands that mimic local and international labels were developed for local rice, and urban consumers bid to upgrade non‐preferred to preferred brands through the Becker–DeGroot–Marschak (BDM) mechanism. Contrary to expectations, results from an endogenous switching regression show that descendants from ancient Senegalese rice domesticators placed premiums on local rice with foreign‐looking brands, indicating that foreignness is perceived as a quality cue even in market segments rooted in cultural heritage. Thus, branding local rice using a combination of local and foreign cues could be an effective strategy in promoting domestic rice to both segments shaped by cultural and colonial heritage.

Morphological variation in bulliform phytoliths at different rice growth stages

Studying morphological changes in bulliform phytoliths in rice during different growth periods can provide essential information for understanding phytolith formation mechanisms and rice domestication processes. In this study, we analysed changes in the size and fish-scale decorations of rice bulliform phytoliths during a complete growth and development cycle. We then explored the underlying plant physiology, agricultural practices, and other factors that influence rice bulliform phytolith formation. From the transplanting stage to the ripening stage, the fan width (HL) and fan length (VL) of bulliform phytoliths tended to increase, decrease, and increase, reaching a maximum at the ripening stage (HL = 40.1 ± 6.1 μm, VL = 39.7 ± 5.3 μm). From the transplanting stage to ripening, the proportion of the long-stalked phenotype decreased significantly, and that of the short-stalked phenotype increased significantly. The proportion of rice bulliform phytoliths with ≥ 9 fish-scale decorations was 0 % at the transplanting and tillering stages and then increased from 42 % to 74 % from the elongation to ripening stage, with an average of 57 % for the four periods (elongation to ripening). The results of this study enhance the existing data on rice phytolith morphology, providing valuable insights into the morphological changes associated with rice domestication.

Mosaic pattern of sustained rice domestication and its environmental and cultural implications in Neolithic East China

China is one of the main locations in which rice agriculture occurs, with East China now playing a significant role in research on rice domestication and culture interactions. However, the exact timing of sustained rice domestication and the process of prehistoric cultural exchange in East China remain unclear. Here, we present phytolith records of two profiles from Lingjiatan in the Chaohu Lake Basin. Our results show that rice cultivation was practiced throughout the Lingjiatan culture period (5800-5300 cal BP), and that sustained rice domestication began around 5500 cal BP, which was later than on the Taihu Plain (∼6200 cal BP), Ningshao Plain (∼5800 cal BP), and along the middle and lower Huai River (∼5800 cal BP). Combining other archaeological records and geomorphological features in East China, we hypothesize three possible routes for the spread of rice cultivation and cultural exchange between the lower Yangtze River and the middle and lower Huai River. Lingjiatan, situated at the intersection of two of the possible routes, experienced a gradual increase in its settled population as a result of cultural exchange and technological innovations in cultivation, thereby giving rise to its distinctive culture. This study demonstrates the significant role of Lingjiatan in facilitating transportation and fostering cultural exchange in East China during the mid-Holocene.

Evolutionary Systems Biology Identifies Genetic Trade-offs In Rice Defense Against Above- and Belowground Attackers.

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, and O. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different above- and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), respectively, and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at the KSL8 and MG1 loci on chromosome 11. KSL8 encodes the first committed step towards biosynthesis of either stemarane- or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking out KSL8-jap and CPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance to S. frugiperda and decreased resistance to M. incognita. Furthermore, MG1 resides in a haplotype that provided resistance to M. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungus Magnaporthe oryzae and other pests and pathogens. Finally, KSL8 and MG1 alleles are located within trans-species haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms at KSL8 and MG1 may be maintained through complex and diffuse community interactions.

Diversity study of several domesticated rice (local cultivars) cultivated in the middle and south of Iraq using NGS technology

نظرًا لأهمية محصول الأرز في العراق ، أجريت هذه الدراسة لتحديد أصول الأصناف الرئيسية وفهم العلاقات التطورية بين أصناف الأرز العراقية وغيرها من انواع الأرز الآسيوية التي يمكن أن تكون ذات اهمية كبيرة في تحسين هذا المحصول. تم الحصول على خمسة أنواع من قسم البحوث الزراعية في العراق, ومن بين هذه الاصناف ( العنبر 33 ، دجلة ، غدير ، البركة ، والأرز الأسود) وقد تم تسلسل الحمض النووي الجيني باكملة باستخدام منصات تسلسل الجيل التالي القائمة على تقنية DNA nanoball (DNB),تم الحصول على تسلسل 26 نوعاً من قاعدة بيانات موارد جينوم NCBI .اظهر التحليل التطوري بنائاً على البلاستيدة الخضراء الانواع قسمت الى مجاميع وفقاً الى موقعهم الجغرافي تم تقسيم الأصناف العراقية إلى مجموعتين المجموعة الاولى تحتوي Amber33 و Japonica NC_001320 بينما تحتوي مجموعة ثانية على Dijla و Ghadir و Baraka و Black Rice و Indica NC_008155.

MicroCT analysis reveals insights into the beginning of rice domestication in the Lower Yangtze during the 10th millennium BP

The Lower Yangtze valley is widely recognized as the earliest center of rice agriculture. The process of rice domestication, based on the morphology of spikelet bases, has been traced between 9000 and 5000 BP. However, the domestication status of rice before 9000 BP remains a subject of debate due to the near absence of macrobotanical remains in the region. This research aims to address this gap by investigating rice impressions and inclusions found in ceramic sherds from Shangshan site, the earliest Neolithic site in the Lower Yangtze valley. Utilizing microCT analysis, this study examined 184 impressions of Oryza sp. spikelet bases from ceramics sherds, generating the most extensive database of rice remains dating to the early Shangshan phase. The results offer valuable insights into the early onset of rice domestication in the Lower Yangtze during the 10th millennium BP. This study represents a pioneering use of microCT analysis of ceramic sherds with early plant impressions.

The First Domesticated 'Cheongju Sorori Rice' Excavated in Korea.

Archaeological excavations led by Yung-jo Lee and Jong-yoon Woo were carried out twice at the Sorori paleolithic site, Cheongju, in the Republic of Korea, at the upper stream of the Geumgang river, the Miho riverside. A total of 127 rice seeds were excavated, including 18 ancient rice and 109 Quasi-rice, in 1998 and 2001. At the first excavation, eleven short japonica-type ancient rice and one slender smooth ancient rice with two kinds of Quasi-rice were excavated. The average length of the 11 short rice grains obtained from the first and second excavation was 7.19 mm and the average width was 3.08 mm, respectively. The Quasi-rice are apparently different from the rice and do not have bi-peak protuberances on their glume surface. At the second excavation, six short ancient rice chaffs and some Quasi-rice 2 were found. These short-grained ancient rice were comparable to the ancient rice that were excavated at the Illsan Neolithic site. Geologists and radiologists confirmed that the peat layer in which the rice found was older than 15,000 years. In this study, the morphological characteristics, crushing, and DNA band patterns related to the genetic polymorphism of rice grains in Cheongju Sorori were compared and analyzed for genetic similarities and differences with wild rice, weed rice, and modern rice. The morphological, ecological, and physiological variations in rice grains excavated from the Sorori site were presumed to denote the origin of rice domestication in Korea. It is also suggested that the results of the DNA sequencing of excavated rice are very important clues in estimating the origin of the early domestication of rice.

DWARF AND LESS TILLERS ON CHROMOSOME 3 promotes tillering in rice by sustaining FLORAL ORGAN NUMBER 1 expression.

Three key factors determine yield in rice (Oryza sativa): panicle number, grain number, and grain weight. Panicle number is strongly associated with tiller number. Although many genes regulating tillering have been identified, whether Dof proteins are involved in controlling plant architecture remains unknown. The dwarf and less tillers on chromosome 3 (dlt3) rice mutant produces fewer tillers than the wild type. We cloned DLT3, which encodes a Dof protein that interacts with MONOCULM 3 (MOC3) in vivo and in vitro and recruits MOC1, forming a DLT3-MOC3-MOC1 complex. DLT3 binds to the promoter of FLORAL ORGAN NUMBER 1 (FON1) to activate its transcription and positively regulate tiller number. The overexpression of MOC1, MOC3, or FON1 in the dlt3 mutant increased tiller number. Collectively, these results suggest a model in which DLT3 regulates tiller number by maintaining the expression of MOC1, MOC3, and FON1. We discovered that DLT3 underwent directional selection in the Xian/indica and Geng/japonica populations during rice domestication. To provide genetic resources for breeding varieties with optimal panicle numbers, we performed large-scale diversity sequencing of the 1,080-bp DLT3 coding region of 531 accessions from different countries and regions. Haplotype analysis showed that the superior haplotype, DLT3H1, produced the most tillers, while haplotype DLT3H6 produced the fewest tillers. Our study provides important germplasm resources for breeding super high-yielding rice varieties with combinations of superior haplotypes in different target genes, which will help overcome the challenge of food and nutritional security in the future.

BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice.

Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

Domestication of rice may have changed its arbuscular mycorrhizal properties by modifying phosphorus nutrition-related traits and decreasing symbiotic compatibility.

Modern cultivated rice (Oryza sativa) typically experiences limited growth benefits from arbuscular mycorrhizal (AM) symbiosis. This could be due to the long-term domestication of rice under favorable phosphorus conditions. However, there is limited understanding of whether and how the rice domestication has modified AM properties. This study compared AM properties between a collection of wild (Oryza rufipogon) and domesticated rice genotypes and investigated the mechanisms underlying their differences by analyzing physiological, genomic, transcriptomic, and metabolomic traits critical for AM symbiosis. The results revealed significantly lower mycorrhizal growth responses and colonization intensity in domesticated rice compared to wild rice, and this change of AM properties may be associated with the domestication modifications of plant phosphorus utilization efficiency at physiological and genomic levels. Domestication also resulted in a decrease in the activity of the mycorrhizal phosphorus acquisition pathway, which may be attributed to reduced mycorrhizal compatibility of rice roots by enhancing defense responses like root lignification and reducing carbon supply to AM fungi. In conclusion, rice domestication may have changed its AM properties by modifying P nutrition-related traits and reducing symbiotic compatibility. This study offers new insights for improving AM properties in future rice breeding programs to enhance sustainable agricultural production.

Identification and Characterization of HS4-Mediated Hybrid Seed Shattering in Rice

Seed shattering is an adaptive feature of seed dispersal in wild rice, and it is also an important agronomic trait affecting yield. Reduced seed shattering was a significant progress during rice domestication. However, the evolutionary pathway and molecular mechanism of hybrid seed shattering remain largely unknown. In order to gain a deeper understanding of the regulation of hybrid seed shattering, HS4, a locus conferring hybrid seed shattering between Oryza sativa and Oryza glaberrima, was identified and fine mapped to a 13.5-kb genomic region containing two putative genes during the development of chromosomal segment substitution lines (CSSLs). Expression analysis indicated that the hybrid seed shattering was not related to the expression of HS4. Preliminary research on the molecular mechanism of HS4-mediated hybrid seed shattering indicated that HS4HJX74 and HS4HP61 may form a multimer in heterozygotes, achieving the original function of a trihelix transcription factor through protein interaction. The identification and characterization of HS4 in this study not only provides new insights into the molecular mechanisms underlying hybrid seed shattering, but also provides a potential target for genome editing to reduce the difficulty of hybridization between the two species, facilitating hybrid breeding and increasing yield in rice.

Rice's trajectory from wild to domesticated in East Asia.

Rice (Oryza sativa) serves as a staple food for more than one-third of the global population. However, its journey from a wild gathered food to domestication remains enigmatic, sparking ongoing debates in the biological and anthropological fields. Here, we present evidence of rice phytoliths sampled from two archaeological sites in China, Shangshan and Hehuashan, near the lower reaches of the Yangtze River. We demonstrate the growth of wild rice at least 100,000 years before present, its initial exploitation as a gathered resource at about 24,000 years before present, its predomestication cultivation at about 13,000 years before present, and eventually its domestication at about 11,000 years before present. These developmental stages illuminate a protracted process of rice domestication in East Asia and extend the continuous records of cereal evolution beyond the Fertile Crescent.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

BackgroundDNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown.ResultsHere, we investigate the variation in DNA methylation during pear domestication and improvement using whole-genome bisulfite sequencing in 41 pear accessions. Contrary to the significant decrease during rice domestication, we detect a global increase in DNA methylation during pear domestication and improvement. We find this specific increase in pear is significantly correlated with the downregulation of Demeter-like1 (DML1, encoding DNA demethylase) due to human selection. We identify a total of 5591 differentially methylated regions (DMRs). Methylation in the CG and CHG contexts undergoes co-evolution during pear domestication and improvement. DMRs have higher genetic diversity than selection sweep regions, especially in the introns. Approximately 97% of DMRs are not associated with any SNPs, and these DMRs are associated with starch and sucrose metabolism and phenylpropanoid biosynthesis. We also perform correlation analysis between DNA methylation and gene expression. We find genes close to the hypermethylated DMRs that are significantly associated with fruit ripening. We further verify the function of a hyper-DMR-associated gene, CAMTA2, and demonstrate that overexpression of CAMTA2 in tomato and pear callus inhibits fruit ripening.ConclusionsOur study describes a specific pattern of DNA methylation in the domestication and improvement of a perennial pear tree and suggests that increased DNA methylation plays an essential role in the early ripening of pear fruits.

The GW5-WRKY53-SGW5 module regulates grain size variation in rice.

Grain size is a crucial agronomic trait that affects stable yield, appearance, milling quality, and domestication in rice. However, the molecular and genetic relationships among QTL genes (QTGs) underlying natural variation for grain size remain elusive. Here, we identified a novel QTG SGW5 (suppressor of gw5) by map-based cloning using an F2 segregation population by fixing same genotype of the master QTG GW5. SGW5 positively regulates grain width by influencing cell division and cell size in spikelet hulls. Two nearly isogenic lines exhibited a significant differential expression of SGW5 and a 12.2% increase in grain yield. Introducing the higher expression allele into the genetic background containing the lower expression allele resulted in increased grain width, while its knockout resulted in shorter grain hulls and dwarf plants. Moreover, a cis-element variation in the SGW5 promoter influenced its differential binding affinity for the WRKY53 transcription factor, causing the differential SGW5 expression, which ultimately leads to grain size variation. GW5 physically and genetically interacts with WRKY53 to suppress the expression of SGW5. These findings elucidated a new pathway for grain size regulation by the GW5-WRKY53-SGW5 module and provided a novel case for generally uncovering QTG interactions underlying the genetic diversity of an important trait in crops.

Comprehensive identification and analysis of DUF640 genes associated with rice growth

Protein domains with conserved amino acid sequences and uncharacterized functions are called domains of unknown function (DUF). The DUF640 gene family plays a crucial role in plant growth, particularly in light regulation, floral organ development, and fruit development. However, there exists a lack of systematic understanding of the evolutionary relationships and functional differentiation of DUF640 within the Oryza genus. In this study, 61 DUF640 genes were identified in the Oryza genus. The expression of DUF640s is induced by multiple hormonal stressors including abscisic acid (ABA), cytokinin (CK), ethylene (ETH), and indole-3-acetic acid (IAA). Specifically, OiDUF640-10 expression significantly increased after ETH treatment. Transgenic experiments showed that overexpressing OiDUF640-10 lines were sensitive to ETH, and seedling length was obstructed. Evolutionary analysis revealed differentiation of the OiDUF640-10 gene in O. sativa ssp. indica and japonica varieties, likely driven by natural selection during the domestication of cultivated rice. These results indicate that OiDUF640-10 plays a vital role in the regulation of rice seedling length.