Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

Genotypic Variation of Purple Rice in Response to Shading in Yield, Anthocyanin Content, and Gene Expression

Purple rice (Oryza sativa L.) contains anthocyanin, which acts as an antioxidant and functional food for humans. The levels of anthocyanin growth and production in rice are mainly controlled by the availability of light. However, shade can affect anthocyanin biosynthesis genes. Therefore, the objective of this study was to determine the yield and anthocyanin content among four purple rice varieties, which provide the difference in colors of purple and green leaves. This study also evaluated gene expression affected by shading treatment to understand the relation of grain anthocyanin and expression level. This research was conducted using a split plot design using four levels of shading (levels of shading from anthesis to maturity) with three replications, no shading, 30% shading, 50% shading, and 70% shading, as the main plots and purple rice varieties as subplots, KJ CMU-107, K2, K4, and KDK10, from anthesis to maturity. Shading significantly decreased yield and yield components, but increased grain anthocyanin content. Nonetheless, the response of yield and grain anthocyanin content to shading did not show a significant different between purple and green leaf varieties. In addition, the level of OsDFR gene expression was different depending on the shading level in four rice varieties. The OsDFR gene presented the highest expression at shading levels of 30% for K4 and 50% for KDK10, while the expression of the OsDFR gene was not detected in the purple rice varieties with green leaves (KJ CMU-107 and K2). The response of grain anthocyanin and gene expression of OsDFR to light treatment did not show significantly differences between the purple and green leaf varieties, suggesting that the appearance of anthocyanin in leaves might be not related to anthocyanin synthesis in the grain. Taken together, the results suggest that some purple rice varieties were more suitable for planting under low light intensity based on a lower level of grain yield loss, strong shade tolerance, and high anthocyanin content in leaf and grain pericarp. However, it is necessary to explore the effects of light intensity on genes and intermediates in the anthocyanin synthesis pathway for further study.

Flavonoid Metabolic Profiles and Gene Mapping of Rice (Oryza sativa L.) Purple Gradient Grain Hulls

Rice (Oryza sativa L.) grain hull color is an easily observable trait and regarded as a crucial morphological marker in rice breeding. Here, a purple gradient grain hull mutant (pg) was found from natural mutations of a straw-white grain hull rice variety IARI 6184B (Orzya sativa L. subsp. indica). The color of the mutant grain hulls changed from straw-white to pink, then purple, and finally brownish-yellow. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified 217 flavonoids, including 18 anthocyanins, among which cyanidin O-syringic acid had the highest concentration in pink (66.2 × 10⁶) and purple (68.0 × 10⁶) grain hulls. The relative contents of hesperetin O-malonyl-hexoside, apigenin derivatives, genistein derivatives, and kaempferol 3-O derivatives were consistently downregulated during pg grain hull development. Conversely, 12 anthocyanins were upregulated in colored hulls, and cyanidin 3-O-malonylhexoside was abundant only in pink and purple grain hulls. Moreover, the candidate gene was mapped into a 1.38 Mb region on chromosome 4 through bulked segregant analysis based on deep sequencing (BSA-seq) and gene mapping approaches. These results increased our understanding of anthocyanin biosynthesis in rice grains, helping rice breeders to select new rice varieties with desirable grain traits.

A novel LOX3-null allele (lox3-b) originated in the aromatic Basmati rice cultivars imparts storage stability to rice bran

Rapid deterioration of rice bran due to the LOX3 enzyme catalysed oxidation of PUFA is the major bottleneck for its utilization in various downstream applications. In the present study, we have identified a set of nine novel LOX3-null rice accessions carrying a deletion of C residue in the exon2 causing a frameshift mutation resulting in a truncated non-functional LOX3 protein. Our study, further manifested the predominance of C deletion based LOX3-null allele, named lox3-b, in the aromatic rice germplasm particularly in the Indian Basmati rice group. The LOX3-null genotypes exhibited significantly reduced rancidity, after six months of storage. They also showed significantly lower percentage reduction of linoleic acid (LA), higher γ-oryzanol content and lower hexanal content. A functional dCAPS marker designed based on the deletion polymorphism clearly differentiated LOX3 and lox3-b alleles, and has the potential application in marker assisted rice breeding programmes to develop cultivars with better bran storability.

The Purple Leaf (pl6) Mutation Regulates Leaf Color by Altering the Anthocyanin and Chlorophyll Contents in Rice

The anthocyanin biosynthesis attracts strong interest due to the potential antioxidant value and as an important morphological marker. However, the underlying mechanism of anthocyanin accumulation in plant tissues is not clearly understood. Here, a rice mutant with a purple color in the leaf blade, named pl6, was developed from wild type (WT), Zhenong 41, with gamma ray treatment. By map-based cloning, the OsPL6 gene was located on the short arm of chromosome 6. The multiple mutations, such as single nucleotide polymorphism (SNP) at −702, −598, −450, an insertion at −119 in the promoter, three SNPs and one 6-bp deletion in the 5′-UTR region, were identified, which could upregulate the expression of OsPL6 to accumulate anthocyanin. Subsequently, the transcript level of structural genes in the anthocyanin biosynthesis pathway, including OsCHS, OsPAL, OsF3H and OsF3′H, was elevated significantly. Histological analysis revealed that the light attenuation feature of anthocyanin has degraded the grana and stroma thylakoids, which resulted in poor photosynthetic efficiency of purple leaves. Despite this, the photoabatement and antioxidative activity of anthocyanin have better equipped the pl6 mutant to minimize the oxidative damage. Moreover, the contents of abscisic acid (ABA) and cytokanin (CK) were elevated along with anthocyanin accumulation in the pl6 mutant. In conclusion, our results demonstrate that activation of OsPL6 could be responsible for the purple coloration in leaves by accumulating excessive anthocyanin and further reveal that anthocyanin acts as a strong antioxidant to scavenge reactive oxygen species (ROS) and thus play an important role in tissue maintenance.

Knockdown of GmVQ58 encoding a VQ motif-containing protein enhances soybean resistance to the common cutworm (Spodoptera litura Fabricius)

Plants have evolved complex defense mechanisms to withstand insect attack. Identification of plant endogenous insect resistance genes is of great significance for understanding plant-herbivore interactions and improving crop insect resistance. Soybean (Glycine max (L.) Merr.) is an important crop that is often attacked by the common cutworm (CCW) (Spodoptera litura Fabricius). In this study, based on our transcriptomic data, the gene GmVQ58, encoding a FxxxVQxxTG (VQ) motif-containing protein, was cloned and characterized. This gene showed the highest expression in the leaves and roots and was up-regulated significantly after CCW attack. Constitutive expression of GmVQ58 rescued the susceptibility of an Arabidopsis mutant to CCW, and interference of GmVQ58 in soybean hairy roots enhanced the resistance to CCW. Furthermore, GmVQ58 was localized to the nucleus and physically interacted with the transcription factor GmWRKY32. The expression of two defense-related genes, GmN:IFR and GmVSPβ, was up-regulated in GmVQ58-RNAi lines. Additionally, the promoter region of GmVQ58 was likely selected during domestication, resulting in different expression patterns in cultivated soybeans relative to wild soybeans. These results suggest that silencing GmVQ58 confers soybean resistance to CCW.

Identification and validation of mutation points associated with waxy phenotype in cassava

BACKGROUND

The granule-bound starch synthase I (GBSSI) enzyme is responsible for the synthesis of amylose, and therefore, its absence results in individuals with a waxy starch phenotype in various amylaceous crops. The validation of mutation points previously associated with the waxy starch phenotype in cassava, as well as the identification of alternative mutant alleles in the GBSSI gene, can allow the development of molecular-assisted selection to introgress the waxy starch mutation into cassava breeding populations.

RESULTS

A waxy cassava allele has been identified previously, associated with several SNPs. A particular SNP (intron 11) was used to develop SNAP markers for screening heterozygote types in cassava germplasm. Although the molecular segregation corresponds to the expected segregation at 3:1 ratio (dominant gene for the presence of amylose), the homozygotes containing the SNP associated with the waxy mutation did not show waxy phenotypes. To identify more markers, we sequenced the GBSS gene from 89 genotypes, including some that were segregated from a cross with a line carrying the known waxy allele. As a result, 17 mutations in the GBSSI gene were identified, in which only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype. The evaluation of mutation points by discriminant analysis of principal component analysis (DAPC) also did not completely discriminate the waxy individuals. Therefore, we developed Kompetitive Allele Specific PCR (KASP) markers that allowed discrimination between WX and wx alleles. The results demonstrated the non-existence of heterozygous individuals of the MeWxEx6-del-C deletion in the analyzed germplasm. Therefore, the deletion MeWxEx6-del-C should not be used for assisted selection in genetic backgrounds different from the original source of waxy starch. Also, the alternative SNPs identified in this study were not associated with the waxy phenotype when compared to a panel of accessions with high genetic diversity.

CONCLUSION

Although the GBSSI gene can exhibit several mutations in cassava, only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype in the original AM206-5 source.

A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population

Increasing agricultural productivity is one of the most important goals of plant science research and imperative to meet the needs of a rapidly growing population. Rice (Oryza sativa L.) is one of the most important staple crops worldwide. Grain size is both a major determinant of grain yield in rice and a target trait for domestication and artificial breeding. Here, a genome-wide association study of grain length and grain width was performed using 996,722 SNP markers in 270 rice accessions. Five and four quantitative trait loci were identified for grain length and grain width, respectively. In particular, the novel grain size gene OsSNB was identified from qGW7, and further results showed that OsSNB negatively regulated grain size. Most notably, knockout mutant plants by CRISPR/Cas9 technology showed increased grain length, width, and weight, while overexpression of OsSNB yielded the opposite. Sequencing of this gene from the promoter to the 3’-untranslated region in 168 rice accessions from a wide geographic range identified eight haplotypes. Furthermore, Hap 3 has the highest grain width discovered in japonica subspecies. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This could be directly used to assist selection toward an improvement of grain width. These findings suggest OsSNB as useful for further improvements in yield characteristics in most cultivars.

Grain weight, including grain length and grain width, is a complex trait, and hundreds of quantitative trait loci (QTLs) were detected in different genetic rice populations. However, only about 10 genes have been isolated and characterized until now. Nine QTLs for grain size were identified by genome-wide association study in a natural rice population. The novel grain size gene OsSNB was identified from qGW7 based on the difference of expression levels between two different varieties with significantly different grain width. OsSNB is an AP2 transcription factor that is negatively regulated grain size. However, OsSNB was found to regulate the transition from the spikelet meristem to the floral meristem and the floral organ development in previous study. Compared to other haplotypes, Hap 3 has a 225 bp insertion in the promoter. Based on the difference between Hap 3 and other haplotypes, OsSNB_Indel2 was designed as a functional marker for the improvement of rice grain width. This can be directly used to assist selection for grain width improvement.

The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice

Floral organs in rice (Oryza sativa) can be purple, brown, or red in color due to the accumulation of flavonoids, but the molecular mechanism underlying specific organ pigmentation is not clear. Here, we propose a C-S-A gene model for rice hull pigmentation and characterize it through genetic, molecular, and metabolomic approaches. Furthermore, we conducted phylogenetic studies to reveal the evolution of rice color. In this gene system, C1 encodes a R2R3-MYB transcription factor and acts as a color-producing gene, and S1 encodes a bHLH protein that functions in a tissue-specific manner. C1 interacts with S1 and activates expression of A1, which encodes a dihydroflavonol reductase. As a consequence, the hull is purple where functional A1 participation leads to high accumulation of cyanidin 3-O-glucoside. Loss of function of A1 leads to a brown hull color due to accumulation of flavonoids such as hesperetin 5-O-glucoside, rutin, and delphinidin 3-O-rutinoside. This shows a different evolutionary pathway of rice color in japonica and indica, supporting independent origin of cultivars in each subspecies. Our findings provide a complete perspective on the gene regulation network of rice color formation and supply the theoretical basis for extended application of this beneficial trait.

Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.

Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice

BACKGROUND

Anthocyanin accumulates in many plant tissues or organs, in rice for example leading to red, purple red and purple phenotypes for protection from damage by biotic and abiotic stresses and for reproduction. Purple leaf, leaf sheath, stigma, pericarp, and apiculus are common in wild rice and landraces and occasionally found in modern cultivars. No gene directly conferring anthocyanin deposited in a purple leaf sheath has yet been isolated by using natural variants. An F2 population derived from ssp. japonica cv. Tainung 72 (TNG72) with purple leaf sheath (PSH) crossed with ssp. indica cv. Taichung Sen 17 (TCS17) with green leaf sheath (GSH) was utilized to isolate a gene conferring leaf sheath color.

RESULTS

By positional cloning, 10-and 3-bp deletions in the R2R3 Myb domain of OsC1 were uncovered in GSH varieties TCS17 and Nipponbare, respectively. Allelic diversity, rather than gene expression levels of OsC1, might be responsible for anthocyanin accumulation. Parsimony-based analysis of genetic diversity in 50 accessions, including cultivars, landraces, and A-genome wild rice, suggests that independent mutation occurred in Asian, African, South American, and Australian species, while O. meridionalis had a divergent sequence. OsC1 was thought of as a domestication related gene, with up to 90 % reduction of genetic diversity in GSH; however, no values from three tests showed significant differences from neutral expectations, implying that OsC1 had not been subjected to recent selection. Haplotype network analysis revealed that species from different continents formed unique haplotypes with no gene flow. Two major groups of haplotypes corresponding to 10-bp deletion and other sequences were formed in Asian rice, including O. rufipogon, O. nivara and O. sativa. Introgressions of OsC1 between subspecies through natural and artificial hybridization were not rare. Because artificial and natural selection imposed admixture on rice germplasm in Taiwan, the genealogy of OsC1 might not be congruent with the current distribution of alleles through lineage diversification.

CONCLUSION

OsC1 is responsible for purple leaf sheath, and much new information about OsC1 is provided e.g., new alleles, non-domestication syndrome, and incongruence of genealogy with geographic distribution.

The Genetic Architecture of Domestication in Animals

Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype.” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.