Chromosome ends initiate homologous chromosome pairing during rice meiosis.

During meiotic prophase I, chromosomes undergo large-scale dynamics to allow homologous chromosome pairing, prior to which chromosome ends attach to the inner nuclear envelope and form a chromosomal bouquet. Chromosome pairing is crucial for homologous recombination and accurate chromosome segregation during meiosis. However, the specific mechanism by which homologous chromosomes recognize each other is poorly understood. Here, we investigated the process of homologous chromosome pairing during early prophase I of meiosis in rice (Oryza sativa) using pooled oligo probes specific to an entire chromosome or chromosome arm. We revealed that chromosome pairing begins from both ends and extends towards the center from early zygotene through late zygotene. Genetic analysis of both trisomy and autotetraploidy also showed that pairing initiation is induced by both ends of a chromosome. However, healed ends that lack the original terminal regions on telocentric and acrocentric chromosomes cannot initiate homologous chromosome pairing, even though they may still enter the telomere clustering region at the bouquet stage. Furthermore, a chromosome that lacks the distal parts on both sides loses the ability to pair with other intact chromosomes. Thus, the native ends of chromosomes play a crucial role in initiating homologous chromosome pairing during meiosis and likely have a substantial impact on genome differentiation.

Development of introgression lines and mapping of qGW2, a novel QTL that confers grain width, in rice (Oryza sativa L.).

Rice grain size is a key determinant of both grain yield and quality. Identification of favorable alleles for use in rice breeding may help to meet the demand for increased yield. In this study, we developed a set of 210 introgression lines (ILs) by using indica variety Huanghuazhan as the donor parent and erect-panicle japonica rice variety Wuyujing3R as the recurrent parent. A total of 133 ILs were selected for high-throughput sequencing. Using specific-locus amplified fragment (SLAF) sequencing technology, 10,103 high-quality SLAF labels evenly distributed on 12 chromosomes were obtained and selected for subsequent analysis. Using a high-density map, quantitative trait locus (QTL) mapping of grain size-related traits was performed, and a total of 38 QTLs were obtained in two environments. Furthermore, qGW2, a novel QTL that controls grain width on chromosome 2, was validated and delimited to a region of 309 kb via substitution mapping. These findings provide new genetic material and a basis for future fine mapping and cloning of favorable QTLs. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01453-0.

A lightweight convolutional neural network hardware implementation for wearable heart rate anomaly detection.

In this article, we propose a lightweight and competitively accurate heart rhythm abnormality classification model based on classical convolutional neural networks in deep neural networks and hardware acceleration techniques to address the shortcomings of existing wearable devices for ECG detection. The proposed approach to build a high-performance ECG rhythm abnormality monitoring coprocessor achieves a high degree of data reuse in time and space, which reduces the number of data flows, provides a more efficient hardware implementation and reduces hardware resource consumption than most existing models. The designed hardware circuit relies on 16-bit floating-point numbers for data inference at the convolutional, pooling, and fully connected layers, and implements acceleration of the computational subsystem through a 21-group floating-point multiplicative-additive computational array and an adder tree. The front- and back-end design of the chip was completed on the TSMC 65 nm process. The device has an area of 0.191 mm2, a core voltage of 1 V, an operating frequency of 20 MHz, a power consumption of 1.1419 mW, and requires 5.12 kByte of storage space. The architecture was evaluated using the MIT-BIH arrhythmia database dataset, which showed a classification accuracy of 97.69% and a classification time of 0.3 ms for a single heartbeat. The hardware architecture offers high accuracy with a simple structure, low resource footprint, and the ability to operate on edge devices with relatively low hardware configurations.

Observation of the effectiveness of clinical indicators of cardiac shock wave therapy in patients with ischemic heart disease: A systematic review and meta-analysis.

Objective: Ischemic heart disease (IHD) has a high prevalence and mortality rate, imposing a heavy burden on patients and society, and there is still a need to optimize treatment options for IHD patients. Cardiac shock wave therapy (CSWT) is gaining popularity as a new treatment for IHD patients. The objective of this meta-analysis is to reassess the effects of CSWT on IHD patients in light of the limited number of clinical studies included in previously published reviews, inconsistent methodological quality, and unclear outcomes. Methods: From database creation until September 1, 2022, 4 English databases and 3 Chinese databases were rigorously searched for any current controlled trials of CSWT for IHD. The Cochrane Risk of Bias Assessment Tool was used for methodological quality assessment. Review Manager v.5.4 software was used for meta-analysis. Results: Nineteen published controlled trials totaling 1,254 subjects were included. Results showed that CSWT could enhance left ventricular function and myocardial viability, improve cardiac function and alleviate angina pectoris symptoms. The effects of CSWT and control groups on SAQ scores and exercise time were not statistically significant. Conclusion: According to this systematic review and meta-analysis, CSWT may be beneficial for a number of IHD clinical indications. To verify these findings, more RCT studies with bigger sample numbers and higher methodological standards are required in the future.

The Effects of Rf4 and the Genetic Mechanism Behind Fertility Restoration of Wild Abortive Cytoplasmic Male Sterility (WA-CMS) in Japonica Rice (Oryza sativa ssp. Japonica).

Wild abortive-type cytoplasmic male sterility (WA-type CMS) has been exclusively used in hybrid seed production in indica rice cultivars, and fertility restoration in WA-type CMS is controlled by two major restorer genes, Rf3 and Rf4, through a sporophytic mechanism. However, the genetic mechanism underlying fertility restoration in WA-type CMS in japonica cultivars is poorly understood. In the present study, C418, a leading Chinsurah Boro II- (BT)-type japonica restorer line, showed partial restoration ability in WA-type japonica CMS lines. The 1:1 segregation ratio of partially fertile to sterile plants in a three-cross F1 population indicated that fertility restoration is controlled by one dominant gene. Gene mapping and sequencing results revealed that the target gene should be Rf4. The Rf4 gene restores fertility through a sporophytic mechanism, but the Rf4 pollen grains show a preferential fertilization in the testcross F1 plants. Furthermore, Rf4 was confirmed to have only a minor effect on fertility restoration in WA-type japonica CMS lines, and Rf gene dosage effects influenced the fertility restoration of WA-type CMS in japonica rice. The results of our study not only provide valuable insights into the complex genetic mechanisms underlying fertility restoration of WA-type CMS but will also facilitate the efficient utilization of WA-type CMS in japonica rice lines.

Different stages of chronic kidney disease are associated with physical performance in adults over 60 years.

Objective: The purpose of this study was to determine the association between different stages of chronic kidney disease (CKD) and sarcopenia and its components in the Chinese older population. Methods: The study comprised of 2,213 participants aged ≥ 60 years (1,025 men; mean age: 70.7 years) recruited from Shanghai who were invited to participate in a comprehensive geriatric assessment. Sarcopenia was defined according to the AWGS 2019 consensus update on sarcopenia diagnosis criteria. The glomerular filtration rate (GFR) was estimated using the equation that originated from the CKD-EPI equation, the stages of CKD are classified according to the Kidney Disease-Improving Global Outcomes (KDIGO). Results: The overall prevalence of sarcopenia was 19.0%, which increased with the severity of CKD. The prevalence of sarcopenia in patients with CKD 3-4 and kidney failure was significantly higher than that in normal and CKD 1-2 (p < 0.05). In logistic regression analysis model, compared with normal and CKD 1 patients, kidney failure was significantly associated with the increased risk of sarcopenia and low grip strength (p < 0.05); CKD 2, CKD 3-4 and kidney failure groups were significantly associated with an increased risk of low walking speed (p < 0.05), respectively; while the association between CKD and muscle mass was not shown. Conclusions: In our study, only decreased physical performance, as represented by walking speed, was significantly associated with increased CKD severity. This may improve the evidence for the prevention and intervention of sarcopenia in patients with CKD.

De novo centromere formation in pericentromeric region of rice chromosome 8.

Neocentromeres develop when kinetochores assemble de novo at DNA loci that are not previously associated with CenH3 nucleosomes, and can rescue rearranged chromosomes that have lost a functional centromere. The molecular mechanisms associated with neocentromere formation in plants have been elusive. Here, we developed a Xian (indica) rice line with poor growth performance in the field due to approximately 272 kb deletion that spans centromeric DNA sequences, including the centromeric satellite repeat CentO, in the centromere of chromosome 8 (Cen8). The CENH3-binding domains were expanded downstream of the original CentO position in Cen8, which revealed a de novo centromere formation in rice. The neocentromere formation avoids chromosomal regions containing functional genes. Meanwhile, canonical histone H3 was replaced by CENH3 in the regions with low CENH3 levels, and the CenH3 nucleosomes in these regions became more periodic. In addition, we identified active genes in the deleted centromeric region, which are essential for chloroplast growth and development. In summary, our results provide valuable insights into neocentromere formation and show that functional genes exist in the centromeric regions of plant chromosomes.

Precise genetic mapping of Rf18(t), a new fertility restorer gene from 'Nipponbare' for wild abortive cytoplasmic male sterility in rice (Oryza sativa L.).

KEY MESSAGE: We mapped Rf18(t), a Restorer-of-fertility gene for wild abortive cytoplasmic male sterility from the japonica maintainer 'Nipponbare', to chromosome 1. The best candidate gene, LOC_Os01g71320, is predicted to encode hexokinase. Three-line hybrid rice obtained through cytoplasmic male sterility (CMS) has helped increase the yield of rice globally, and the wild abortive (WA)-type cytoplasm from wild rice (Oryza rufipogon Griff.) is used widely in three-line indica hybrids. The identification and mapping of the Restorer-of-fertility (Rf) genes in maintainer lines aided in uncovering the genetic basis of fertility restoration of WA-type CMS and the development of WA-type hybrids. In this study, we identified a new Rf gene, Rf18(t), for WA-type CMS from the japonica maintainer line 'Nipponbare' using a chromosome segment substitution line population derived from a cross between the indica line 9311 and 'Nipponbare.' Using a substitution mapping strategy, Rf18(t) was delimited to a 48-kb chromosomal region flanked by molecular marker loci ID01M28791 and ID01M28845 on chromosome 1. By comparative sequence analyses, we propose that LOC_Os01g71320 is the most likely candidate gene for Rf18(t), and it is predicted to encode hexokinase. Furthermore, Rf18(t) was found to function in fertility restoration probably by a posttranscriptional mechanism and its function is dependent on the genetic background of 9311. These results broaden our knowledge on the mechanism of fertility restoration of WA-type CMS lines and will facilitate the development of WA-type rice hybrids.

A 65nm/0.448 mW EEG processor with parallel architecture SVM and lifting wavelet transform for high-performance and low-power epilepsy detection.

In recent years, low-power and wearable biomedical testing devices have emerged as a key answer to the challenges associated with epilepsy disorders, which are prone to crises and require prolonged monitoring. The feature vector of the electroencephalographic (EEG) signal was extracted using the lifting wavelet transform algorithm, and the hardware of the lifting wavelet transform module was optimized using the canonic signed digit (CSD) coding method. A low-power EEG feature extraction circuit with a power consumption of 0.42 mW was constructed. This article employs the support vector machine (SVM) technique after feature extraction to categorize and identify epilepsy. A parallel SVM processing unit was constructed to accelerate classification and identification, and then a high-speed, low-power EEG epilepsy detection processor was implemented. The processor design was completed using TSMC 65 nm technology. The chip size is 0.98 mm2, operating voltage is 1 V, operating frequency is 1 MHz, epilepsy detection latency is 0.91 s, power consumption is 0.448 mW, and energy efficiency of a single classification is 2.23 µJ/class. The CHB-MIT database test results show that this processor has a sensitivity of 91.86% and a false detection rate of 0.17/h. Compared to other processors, this processor is more suitable for portable/wearable devices.

Research progress of plant cytogenetics in Jiangsu province.

Cytogenetics was established based on the "Chromosome theory of inheritance", proposed by Boveri and Sutton and evidenced by Morgan's lab in early stage of the 20 th centrary. With rapid development of related research areas, especially molecular genetics, cytogenetics developed from traditional into a new era, molecular cytogenetics in late 1960s. Featured by an established technique named DNA in situ hybridization (ISH), molecular cytogenetics has been applied in various research areas. ISH provids vivid and straightforward figures showing the virtual presence of DNA, RNA or proteins. In combination with genomics and cell biology tools, ISH and derived techniques have been widely used in studies of the origin, evolution, domestication of human, animal and plant, as well as wide hybridization and chromosome engineering. The physical location and order of DNA sequences revealed by ISH enables the detection of chromosomal re-arrangments among related species and gaps of assembled genome sequences. In addition, ISH using RNA or protein probes can reveal the location and quantification of transcripted RNA or translated protein. Since the 1970s, scientists from universities or institutes belonging to the Jiangsu Society of Genetics have initiated cytogenetics researches using various plant species. In recent years, research platforms for molecular cytogenetics have also been well established in Nanjing Agricultural University, Yangzhou University, Nanjing Forestry University, Jiangsu Xuhuai Academy of Agricultural Sciences, and Jiangsu Normal University. The application of molecular cytogenetics in plant evolution, wide hybridization, chromosome engineering, chromosome biology, genomics has been successful. Significant progresses have been achieved, both in basic and applied researches. In this paper, we will review main research progresses of plant cytogenetics in Jiangsu province, and discuss the potential development of this research area.

Progress on inheritance and gene cloning for rice grain quality in Jiangsu province.

In China, rice (Oryza sativa L.) is a major cereal crop of great importance maintaining the food security and sustainable agricultural development. Jiangsu is one of the main provinces for rice production. After more than 40 years of development, the yield and quality of rice grain have made great progress. Rice grain quality is a complex trait involving production, processing, marketing and consumption of the grain. In this review, we summarize the progress on the genetic basis of main grain quality traits in the rice variety breeding in Jiangsu province and point out the achievement of each milestone. With a focus on the genetic regulation of grain appearance, eating and cooking quality and nutritional quality, we describe the classic genetic rules and molecular basis of rice grain quality traits and review the function of major genes that regulate corresponding traits. The genetics and improvement of grain quality achieved in Jiangsu province was highlighted on the domestic and international rice breeding programs. In particular, with the advance of breeding conception in terms of functional genomics and genetic regulatory networks, the specific molecular design for grain quality improvement will be the future direction of rice genetic breeding program of Jiangsu Province.

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency.

In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb . We validated the effects of Wxmw on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.

OsPP2C09, a negative regulatory factor in abscisic acid signalling, plays an essential role in balancing plant growth and drought tolerance in rice.

Plants maintain a dynamic balance between plant growth and stress tolerance to optimise their fitness and ensure survival. Here, we investigated the roles of a clade A type 2C protein phosphatase (PP2C)-encoding gene, OsPP2C09, in regulating the trade-off between plant growth and drought tolerance in rice (Oryza sativa L.). The OsPP2C09 protein interacted with the core components of abscisic acid (ABA) signalling and showed PP2C phosphatase activity in vitro. OsPP2C09 positively affected plant growth but acted as a negative regulator of drought tolerance through ABA signalling. Transcript and protein levels of OsPP2C09 were rapidly induced by exogenous ABA treatments, which suppressed excessive ABA signalling and plant growth arrest. OsPP2C09 transcript levels in roots were much higher than those in shoots under normal conditions. After ABA, polyethylene glycol and dehydration treatments, the accumulation rate of OsPP2C09 transcripts in roots was more rapid and greater than that in shoots. This differential expression between the roots and shoots may increase the plant's root-to-shoot ratio under drought-stress conditions. This study sheds new light on the roles of OsPP2C09 in coordinating plant growth and drought tolerance. In particular, we propose that OsPP2C09-mediated ABA desensitisation contributes to root elongation under drought-stress conditions in rice.

COM1, a factor of alternative non-homologous end joining, lagging behind the classic non-homologous end joining pathway in rice somatic cells.

The role of rice (Oryza sativa) COM1 in meiotic homologous recombination (HR) is well understood, but its part in somatic double-stranded break (DSB) repair remains unclear. Here, we show that for rice plants COM1 conferred tolerance against DNA damage caused by the chemicals bleomycin and mitomycin C, while the COM1 mutation did not compromise HR efficiencies and HR factor (RAD51 and RAD51 paralogues) localization to irradiation-induced DSBs. Similar retarded growth at the post-germination stage was observed in the com1-2 mre11 double mutant and the mre11 single mutant, while combined mutations in COM1 with the HR pathway gene (RAD51C) or classic non-homologous end joining (NHEJ) pathway genes (KU70, KU80, and LIG4) caused more phenotypic defects. In response to γ-irradiation, COM1 was loaded normally onto DSBs in the ku70 mutant, but could not be properly loaded in the MRE11RNAi plant and in the wortmannin-treated wild-type plant. Under non-irradiated conditions, more DSB sites were occupied by factors (MRE11, COM1, and LIG4) than RAD51 paralogues (RAD51B, RAD51C, and XRCC3) in the nucleus of wild-type; protein loading of COM1 and XRCC3 was increased in the ku70 mutant. Therefore, quite differently to its role for HR in meiocytes, rice COM1 specifically acts in an alternative NHEJ pathway in somatic cells, based on the Mre11-Rad50-Nbs1 (MRN) complex and facilitated by PI3K-like kinases. NHEJ factors, not HR factors, preferentially load onto endogenous DSBs, with KU70 restricting DSB localization of COM1 and XRCC3 in plant somatic cells.

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species.

Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs of rice chromosomes. Standard karyotypes of rice were established using this system on both mitotic and meiotic chromosomes. Moreover, dual-color oligo-FISH was used to characterize diverse chromosomal abnormalities. Oligo-FISH analyses using these probes in various wild Oryza species revealed that chromosomes from the AA, BB or CC genomes generated specific and intense signals similar to those in rice, while chromosomes with the EE genome generated less specific signals and the FF genome gave no signal. Together, the oligo-FISH probes we established will be a powerful tool for studying chromosome variations and evolution in the genus Oryza.

Clinical characteristics and phenotype distribution in 10 Chinese patients with X-linked adrenoleukodystrophy.

X-linked adrenoleukodystrophy (X-ALD) is the most frequent type of inherited demyelinating peroxisomal disease caused by mutations in the ATP binding cassette subfamily D member 1 (ABCD1) gene. The rate of early recognition and genetic diagnosis of X-ALD remains low due to its variable clinical manifestations. The present study summarized the clinical features Chinese X-ALD patients and performed a follow-up study to further precisely characterize this disease. A total of 10 patients diagnosed with X-ALD between 1994 and 2016 at Shandong Provincial Hospital Affiliated to Shandong University (Jinan, China) were included in the present study. Through reviewing their medical records and performing telephone follow-ups, the clinical features, biochemical laboratory data, brain images, treatments and long-term outcomes were retrospectively summarized. Mutation analysis of the ABCD1 gene was performed in certain patients. Most of the patients (8/10) had the childhood cerebral form of X-ALD. One patient presented with the olivo-ponto-cerebellar form, the rarest form of X-ALD. In all patients, brain magnetic resonance images revealed abnormalities with typical T2-weighted hyperintensity. Analysis of very long chain fatty acid revealed high plasma levels of hexacosanoic acid in all patients. Increased adrenocorticotropic hormone, decreased cortisol and neurophysiological manifestations were also observed. Three different mutations of the ABCD1 gene were identified in the 3 patients subjected to genotyping. During the follow-ups, most patients took neurotrophic drugs and received hydrocortisone replacement when required. One patient received a hematopoietic stem cell transplantation, but died 1 year following the transplantation. Chronic myelopathy and peripheral neuropathy progressed with time, gradually leading to a vegetative state or paralysis within several years of clinical symptom onset. In conclusion, male patients with adrenocortical insufficiency should be further investigated for X-ALD. Early detection is critical to prevent the progression of X-ALD with mutation analysis of ABCD1 the most accurate method to confirm diagnosis.

The heterotrimeric G protein ß subunit RGB1 is required for seedling formation in rice.

BACKGROUND: The heterotrimeric G protein ß subunit RGB1 plays an important role in plant growth and development. However, the molecular mechanisms underlying the regulation of rice growth by RGB1 remain elusive. RESULTS: Here, the rgb1 mutants rgb1-1 (+ 1 bp), rgb1-2 (- 1 bp), and rgb1-3 (- 11 bp) were isolated using the CRISPR/Cas9 system, and they were arrested at 1 day after germination and ultimately exhibited seedling lethality. The dynamic anatomical characteristics of the embryos of the rgb1 seedlings and WT during early postgermination and according to TUNEL assays showed that the suppressed growth of the rgb1 mutants was caused by cell death. In addition to the limited shoot and root development, the development of the embryo shoot-root axis was suppressed in the rgb1 mutants. RGB1 was expressed mainly in the root epidermal and vascular tissues of the embryo. Moreover, transcript profiling analysis revealed that the expression of a large number of auxin-, cytokinin-, and brassinosteroid-inducible genes was upregulated or downregulated in the rgb1 mutant compared to the wild type during seedling development. CONCLUSIONS: Overall, the rgb1 mutants provide an ideal material for exploring the molecular mechanism underlying rice seedling formation during early postgermination development by G proteins. SIGNIFICANCE STATEMENT: The heterotrimeric G protein ß subunit RGB1 acts as a crucial factor in promoting early postgermination seedling development in rice.

The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions.

BACKGROUND: Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC. RESULTS: We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wxb allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3ind into the soft rice variety Nangeng9108 with Wxmq, a mutant allele of Wxb, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice. CONCLUSIONS: Our results indicate that the qSAC3ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wxmq allele.

Wxlv, the Ancestral Allele of Rice Waxy Gene.

In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wxlv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.

Natural variation of OsGluA2 is involved in grain protein content regulation in rice.

Grain protein content (GPC) affects rice nutrition quality. Here, we identify two stable quantitative trait loci (QTLs), qGPC-1 and qGPC-10, controlling GPC in a mapping population derived from indica and japonica cultivars crossing. Map-based cloning reveals that OsGluA2, encoding a glutelin type-A2 precursor, is the candidate gene underlying qGPC-10. It functions as a positive regulator of GPC and has a pleiotropic effect on rice grain quality. One SNP located in OsGluA2 promoter region is associated with its transcript expression level and GPC diversity. Polymorphisms of this nucleotide can divide all haplotypes into low (OsGluA2LET) and high (OsGluA2HET) expression types. Population genetic and evolutionary analyses reveal that OsGluA2LET, mainly present in japonica accessions, originates from wild rice. However, OsGluA2HET, the dominant type in indica, is acquired through mutation of OsGluA2LET. Our results shed light on the understanding of natural variations of GPC between indica and japonica subspecies.