Control of grain size in rice

Small grain and semi-dwarf 3, a WRKY transcription factor, negatively regulates plant height and grain size by stabilizing SLR1 expression in rice

OsWRKY36 represses plant height and grain size by inhibiting gibberellin signaling. Plant height and grain size are important agronomic traits affecting yield in cereals, including rice. Gibberellins (GAs) are plant hormones that promote plant growth and developmental processions such as stem elongation and grain size. WRKYs are transcription factors that regulate stress tolerance and plant development including height and grain size. However, the relationship between GA signaling and WRKY genes is still poorly understood. Here, we characterized a small grain and semi-dwarf 3 (sgsd3) mutant in rice cv. Hwayoung (WT). A T-DNA insertion in the 5'-UTR of OsWRKY36 induced overexpression of OsWRKY36 in the sgsd3 mutant, likely leading to the mutant phenotype. This was confirmed by the finding that overexpression of OsWRKY36 caused a similar small grain and semi-dwarf phenotype to the sgsd3 mutant whereas knock down and knock out caused larger grain phenotypes. The sgsd3 mutant was also hyposensitive to GA and accumulated higher mRNA and protein levels of SLR1 (a GA signaling DELLA-like inhibitor) compared with the WT. Further assays showed that OsWRKY36 enhanced SLR1 transcription by directly binding to its promoter. In addition, we found that OsWRKY36 can protect SLR1 from GA-mediated degradation. We thus identified a new GA signaling repressor OsWRKY36 that represses GA signaling through stabilizing the expression of SLR1.

Characterization of the 'Oat-Like Rice' Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L

BACKGROUND

Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield.

RESULTS

Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs, an open hull formed by remarkably elongated leafy lemmas and paleae, occasionally formed conjugated twin brown rice, an aberrant grain shape and a low seed setting rate. By map-based cloning, we discovered that Oat-like rice harbors a novel allele of OsMADS1 gene (OsMADS1^Olr), which has a spontaneous point mutation that causes the substitution of an amino acid that is highly conserved in the MADS-box domain of the MADS-box family. Further linkage analysis indicated that the point mutation in the OsMADS1^Olr is associated with Oat-like rice phenotype, and expression analysis of the OsMADS1 by qRT-PCR and GUS staining also indicated that it is highly expressed in flower organs as well as in the early stages of grain development. Furthermore, OsMADS1^Olr-overexpressing plants showed similar phenotypes of Oat-like rice in grain shape, possibly due to the dominant negative effect. And OsMADS1-RNAi plants also displayed grain phenotypes like Oat-like rice. These results suggested that OsMADS1^Olr is responsible for the Oat-like rice phenotype including aberrant grain shape. Moreover, the expression levels of representative genes related to grain shape regulation were apparently altered in Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi transgenic plants. Finally, compared with Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants, mild phenotype of seed-specific OsMADS1-RNAi transgenic plants indicated that OsMADS1 may has has a direct regulation role in grain development and the grain phenotypes of Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants are majorly caused by the abnormal lemma and palea development.

CONCLUSIONS

Altogether, our results showed that grain shape and a low seed setting rate of the notable 'Oat-like rice' are caused by a spontaneous point mutation in the novel allele OsMADS1^Olr. Furthermore, our findings suggested that OsMADS1 mediates grain shape possibly by affecting the expression of representative genes related to grain shape regulation. Thus, this study not only revealed that OsMADS1 plays a vital role in regulating grain shape of rice but also highlighted the importance and value of OsMADS1 to improve the quality and yield of rice by molecular breeding.

Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size

Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.

RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat

Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.

gw2 mutation increases grain width and culm thickness in rice (Oryza sativa L.)

Grain size is one of the most important agricultural traits in rice. To increase grain yield, we screened a large grain mutant from mutants with the 'Koshihikari' background. As a result, we obtained a mutant, KEMS39, that has a large grain size and increased yield. Cultivation tests revealed that this mutant had improved lodging resistance with thicker internodes. Next-generation sequencing analysis revealed the presence of a 67 bp deletion in the GW2 mRNA, owing to a mutation in the 3' splice site of the sixth intron of the GW2 gene. To determine whether this mutation was responsible for the larger grain and thicker internodes, we performed gene editing and obtained a mutant with a 7 bp deletion, including this 3' splice site. As this gw2 mutant had large grains and thicker internodes, the causal gene of KEMS39 was determined as GW2. Thicker internodes are attributed to the pleiotropic effect of gw2 mutation. On the basis of these results, we conclude that gw2 mutation has the potential to be an important genetic resource with the ability to achieve a well-balanced and high-yielding effect that simultaneously improves grain productivity and lodging resistance.

Rice yield formation under high day and night temperatures-A prerequisite to ensure future food security

Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.

The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division

Grain size is a major determinant of cereal grain yields; however, the relevant regulatory mechanisms controlling this trait have not been fully elucidated. The rice (Oryza sativa) mutant short grain6 (sg6) was identified based on its reduced grain length and weight. Here, we functionally characterized the role of SG6 in determining grain size through the regulation of spikelet hull cell division. SG6 encodes a previously uncharacterized plant AT-rich sequence and zinc-binding (PLATZ) protein that is ubiquitously localized throughout the cell and is preferentially expressed in the early developing panicles but not in the endosperm. The overexpression of SG6 resulted in significantly larger and heavier grains, as well as increased plant heights, which is consistent with its elevated spikelet hull cell division rate. Yeast two-hybrid analyses revealed that SG6 interacts with the core cell cycle machinery DP protein and several other putative cell division regulators, consistent with our transcriptomic analysis, which showed that SG6 activates the expression of many DNA replication and cell-cycle-related genes. These results confirm the crucial role of SG6 in determining grain size by regulating spikelet hull cell division and provide clues for understanding the functions of PLATZ family proteins and the network regulating cereal grain size.

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia

We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.

Training instance segmentation neural network with synthetic datasets for crop seed phenotyping

In order to train the neural network for plant phenotyping, a sufficient amount of training data must be prepared, which requires time-consuming manual data annotation process that often becomes the limiting step. Here, we show that an instance segmentation neural network aimed to phenotype the barley seed morphology of various cultivars, can be sufficiently trained purely by a synthetically generated dataset. Our attempt is based on the concept of domain randomization, where a large amount of image is generated by randomly orienting the seed object to a virtual canvas. The trained model showed 96% recall and 95% average Precision against the real-world test dataset. We show that our approach is effective also for various crops including rice, lettuce, oat, and wheat. Constructing and utilizing such synthetic data can be a powerful method to alleviate human labor costs for deploying deep learning-based analysis in the agricultural domain.

OsINV3 and Its Homolog, OsINV2, Control Grain Size in Rice

Vacuolar invertase is involved in sugar metabolism and plays a crucial role in plant growth and development, thus regulating seed size. However, information linking vacuolar invertase and seed size in rice is limited. Here we characterized a small grain mutant sg2 (grain size on chromosome 2) that showed a reduced in grain size and 1000-grain weight compared to the wild type. Map-based cloning and genetic complementation showed that OsINV3 is responsible for the observed phenotype. Loss-of-function of OsINV3 resulted in grains of smaller size when compared to the wild type, while overexpression showed increased grain size. We also obtained a T-DNA insertion mutant of OsINV2, which is a homolog of OsINV3 and generated double knockout (KO) mutants of OsINV2 and OsINV3 using CRISPR/Cas9. Genetic data showed that OsINV2, that has no effect on grain size by itself, reduces grain length and width in the absence of OsINV3. Altered sugar content with increased sucrose and decreased hexose levels, as well as changes vacuolar invertase activities and starch constitution in INV3^KO, INV2^KO, INV3^KOINV2^KO mutants indicate that OsINV2 and OsINV3 affect sucrose metabolism in sink organs. In summary, we identified OsINV3 as a positive regulator of grain size in rice, and while OsINV2 has no function on grain size by itself. In the absence of OsINV3, it is possible to detect a role of OsINV2 in the regulation of grain size. Both OsINV3 and OsINV2 are involved in sucrose metabolism, and thus regulate grain size. Our findings increase our understanding of the role of OsINV3 and its homolog, OsINV2, in grain size development and also suggest a potential strategy to improve grain yield in rice.

Quantitative Trait Loci for Seed Size Variation in Cucurbits - A Review

Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV-associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.

The shape of things to come: ovate family proteins regulate plant organ shape

The shape of produce is an important agronomic trait. The knowledge of the cellular regulation of organ shapes can be implemented in the improvement of a variety of crops. The plant-specific Ovate Family Proteins (OFPs) regulate organ shape in Arabidopsis and many crops including rice, tomato, and melon. Although OFPs were previously described as transcriptional repressors, recent data support a role for the family in organ shape regulation through control of subcellular localization of protein complexes. OFPs interact with TONNEAU1 RECRUITMENT MOTIF (TRMs) and together they regulate cell division patterns in tomato fruit development. OFPs also respond to changes in plant hormones and responses to stress. The OFP-TRM interaction may work in conjunction with additional shape regulators such as IQ67 Domain (IQD) proteins to modulate the response to tissue level cues as well as external stimuli and stressors to form reproducible organ shapes by regulating cytoskeleton activities.

Divergent phenotypic response of rice accessions to transient heat stress during early seed development

Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well-documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating the HS response during early seed development. To explore the variation in HS sensitivity, we investigated aus (1), indica (2), temperate japonica (2), and tropical japonica (4) accessions for their HS (39/35°C) response during early seed development that accounts for transition of endosperm from syncytial to cellularization, which broadly corresponds to 24 and 96 hr after fertilization (HAF), respectively, in rice. The two indica and one of the tropical japonica accessions exhibited severe heat sensitivity with increased seed abortion; three tropical japonicas and an aus accession showed moderate heat tolerance, while temperate japonicas exhibited strong heat tolerance. The accessions exhibiting extreme heat sensitivity maintain seed size at the expense of number of fully developed mature seeds, while the accessions showing relative resilience to the transient HS maintained number of fully developed seeds but compromised on seed size, especially seed length. Further, histochemical analysis revealed that all the tested accessions have delayed endosperm cellularization upon exposure to the transient HS by 96 HAF; however, the rate of cellularization was different among the accessions. These findings were further corroborated by upregulation of cellularization-associated marker genes in the developing seeds from the heat-stressed samples.

Harnessing Transcription Factors as Potential Tools to Enhance Grain Size Under Stressful Abiotic Conditions in Cereal Crops

Predicted climate change is widely cited to significantly reduce yields of the major cereal crop species in a period where demand is rapidly rising due to a growing global population. This requires exhaustive research to develop genetic resources in order to address the expected production deficiencies which will largely be driven by abiotic stress. Modification of multiple genes is an approach that can address the predicted challenges; however, it is time-consuming and costly to modify multiple genes simultaneously. Transcription factors represent a group of proteins regulating multiple genes simultaneously and are therefore promising targets to concurrently improve multiple traits concurrently, such as abiotic stress tolerance and grain size (a contributor to yield). Many studies have identified the complex role that transcription factors of multiple families have contributed toward abiotic stress tolerance or grain size, although research addressing both simultaneously is in its infancy despite its potential significance for cereal crop improvement. Here we discuss the potential role that transcription factors may contribute toward improving cereal crop productivity under adverse environmental conditions and offer research objectives that need to be addressed before the modification of transcription factors becomes routinely used to positively manipulate multiple target traits.

Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective

The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.

GW5-Like, a homolog of GW5, negatively regulates grain width, weight and salt resistance in rice

Grain size is an important determinant of yield potential in crops. We previously demonstrated that natural mutations in the regulatory sequences of qSW5/GW5 confer grain width diversity in rice. However, the biological function of a GW5 homolog, named GW5-Like (GW5L), remains unknown. In this study, we report on GW5L knockout mutants in Kitaake, a japonica cultivar (cv.) considered to have a weak gw5 variant allele that confers shorter and wider grains. GW5L is evenly expressed in various tissues, and its protein product is localized to the plasma membrane. Biochemical assays verified that GW5L functions in a similar fashion to GW5. It positively regulates brassinosteroid (BR) signaling through repression of the phosphorylation activity of GSK2. Genetic data show that GW5L overexpression in either Kitaake or a GW5 knockout line, Kasa^orf3 (indica cv. Kasalath background), causes more slender, longer grains relative to the wild-type. We also show that GW5L could confer salt stress resistance through an association with calmodulin protein OsCaM1-1. These findings identify GW5L as a negative regulator of both grain size and salt stress tolerance, and provide a potential target for breeders to improve grain yield and salt stress resistance in rice.

The nutrient distribution in the continuum of the pericarp, seed coat, and kernel during Styrax tonkinensis fruit development

Background

Styrax tonkinensis is a great potential biofuel as the species contains seeds with a particularly high oil content. Understanding the nutrient distribution in different parts of the fruit is imperative for the development and enhancement of S. tonkinensis as a biodiesel feedstock.

Methods

From 30 to 140 days after flowering (DAF), the development of S. tonkinensis fruit was tracked. The morphology change, nutrient content, and activity of associated enzymes in the continuum of the pericarp, seed coat, and kernel were analyzed.

Results

Between 30 and 70 DAF, the main locus of dry matter deposition shifted from the seed coat to the kernel. The water content within the pericarp remained high throughout development, but at the end (130 DAF later) decreased rapidly. The water content within both the seed coat and the kernel consistently declined over the course of the fruit development (30–110 DAF). Between 70 and 80 DAF, the deposition centers for sugar, starch, protein, potassium, and magnesium was transferred to the kernel from either the pericarp or the seed coat. The calcium deposition center was transferred first from pericarp to the seed coat and then to the kernel before it was returned to the pericarp. The sucrose to hexose ratio in the seed coat increased between 30 and 80 DAF, correlating with the accumulation of total soluble sugar, starch, and protein. In the pericarp, the sucrose to hexose ratio peaked at 40 and 100 DAF, correlating with the reserve deposition in the following 20–30 days. After 30 DAF, the chlorophyll concentration of both the pericarp and the seed coat dropped. The maternal unit (the pericarp and the seed coat) in fruit showed a significant positive linear relationship between chlorophyll b/a and the concentration of total soluble sugar. The potassium content had significant positive correlation with starch (ρ = 0.673, p = 0.0164), oil (ρ = 0.915, p = 0.000203), and protein content (ρ = 0.814, p = 0.00128), respectively. The concentration of magnesium had significant positive correlation with starch (ρ = 0.705, p = 0.0104), oil (ρ = 0.913, p = 0.000228), and protein content (ρ = 0.896, p = 0.0000786), respectively. Calcium content had a significant correlation with soluble sugar content (ρ = 0.585, p = 0.0457).

Conclusions

During the fruit development of S. tonkinensis, the maternal unit, that is, the pericarp and seed coat, may act a nutrient buffer storage area between the mother tree and the kernel. The stage of 70–80 DAF is an important time in the nutrient distribution in the continuum of the pericarp, seed coat, and kernel. Our results described the metabolic dynamics of the continuum of the pericarp, seed coat, and kernel and the contribution that a seed with high oil content offers to biofuel.

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.

OsGASR9 positively regulates grain size and yield in rice (Oryza sativa)

The plant-specific gibberellic acid (GA)-stimulated transcript gene family is critical for plant growth and development. There are 10 family members in rice (Oryza sativa), known as OsGASRs. However, few have been functionally characterized. Here, we investigated the function of OsGASR9 in rice. OsGASR9 transcripts were detected in various tissues, with the lowest and highest levels in leaves and panicles, respectively. Greater mRNA levels accumulated in young, compared with in old, panicles and spikelets. OsGASR9 localized to the plasma membrane, cytoplasm and nucleus. Transgenic RNA interference-derived lines in the Zhonghua 11 background exhibited reduced plant height, grain size and yield compared with the wild-type. The two osgasr9 mutants in the Nipponbare background showed similar phenotypes. Conversely, the overexpression of OsGASR9 in the two backgrounds increased plant height and grain size. A significantly increased grain yield per plant was also observed in the overexpression lines having a Nipponbare background. Furthermore, by measuring the GA-induced lengths of the second leaf sheaths and α-amylase activity levels of seeds, we concluded that OsGASR9 is a positive regulator of responses to GA in rice. Thus, OsGASR9 may regulate plant height, grain size and yield through the GA pathway and could have an application value in breeding.

Genome-wide identification of circular RNAs in peanut (Arachis hypogaea L.)

Background

Circular RNAs (circRNAs), a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and developmental processes in eukaryotic cells. However, there have been no related studies on the number of circRNAs and their overall characteristics including circRNA abundance and expression profiles in peanut, which is one of the most important edible oil seed crops in the world.

Results

We performed a genome-wide identification of circular RNAs using ribosomal-depleted RNA-sequencing from the seeds of two peanut eighth-generation recombinant inbred lines (RIL8): ‘RIL 8106’ (a medium-pod variety) and ‘RIL 8107’ (a super-pod variety), at 15 and 35 days after flowering (DAF), respectively. A total of 347 circRNA candidates were detected by two computational pipelines: CIRCexplorer and CIRI, with at least two supporting junction reads. All these circRNAs were generated from exons of annotated genes, and widespread on the 20 peanut chromosomes. The expression profiles revealed that circRNAs were differentially expressed between two stages and between two lines. GO enrichment analysis of the host genes produced differentially-expressed circRNAs suggested that circRNAs are involved in seed development and regulation of seed size. Fifteen circRNAs were experimentally analyzed by qRT-PCR with divergent primers, and six circRNAs were resistant to digestion with RNase R exonuclease, and the back-splicing sites were further validated by Sanger DNA sequencing.

Conclusions

We present the first systematical investigation of the genomic characteristics and expression profiles of circRNAs in peanut. The results revealed that circRNAs are abundant and widespread in peanut, and the differentially-expressed circRNAs between two lines suggested that they might play regulatory roles in peanut seeds development.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6020-7) contains supplementary material, which is available to authorized users.

Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

Background

Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100–RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location.

Method

A total of 12 populations were used. The ZC9 population comprised 203 S_1:2 families derived from a residual heterozygous (RH) plant in the F₉ generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100–RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S₁ plants derived from one RH plant in F₇ of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100–RM228. The other ten populations were all derived from Ti52-1, including five S₁ populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM.

Result

Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704–RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions.

Conclusion

Three QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction.

Dissecting the Genetic Basis of Grain Size and Weight in Barley (Hordeum vulgare L.) by QTL and Comparative Genetic Analyses

Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.

LARGE GRAIN Encodes a Putative RNA-Binding Protein that Regulates Spikelet Hull Length in Rice

Grain size is a key determiner of grain weight, one of the yield components in rice (Oryza sativa). Therefore, to increase grain yield, it is important to elucidate the detailed mechanisms regulating grain size. The Large grain (Lgg) mutant, found in the nonautonomous DNA-based active rice transposon1 (nDart1)-tagged lines of Koshihikari, is caused by a truncated nDart1-3 and 355 bp deletion in the 5' untranslated region of LGG, which encodes a putative RNA-binding protein, through transposon display and cosegregation analysis between grain length and LGG genotype in F2 and F3. Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9-mediated knockout and overexpression of LGG led to longer and shorter grains than wild type, respectively, showing that LGG regulates spikelet hull length. Expression of LGG was highest in the 0.6-mm-long young panicle and gradually decreased as the panicle elongated. LGG was also expressed in roots and leaves. These results show that LGG functions at the very early stage of panicle development. Longitudinal cell numbers of spikelet hulls of Lgg, knockout and overexpressed plants were significantly different from those of the wild type, suggesting that LGG might regulate longitudinal cell proliferation in the spikelet hull. RNA-Seq analysis of 1-mm-long young panicles from LGG knockout and overexpressing plants revealed that the expressions of many cell cycle-related genes were reduced in knockout plants relative to LGG-overexpressing plants and wild type, whereas some genes for cell proliferation were highly expressed in knockout plants. Taken together, these results suggest that LGG might be a regulator of cell cycle and cell division in the rice spikelet hull.

Evaluation of differential qPE9-1/DEP1 protein domains in rice grain length and weight variation

BACKGROUND

qPE9-1/DEP1, encoding a G protein γ subunit, has multiple effects on plant architecture, grain size, and yield in rice. The qPE9-1 protein contains an N-terminal G gamma-like (GGL) domain, a putative transmembrane domain, and a C-terminal cysteine-rich domain. However, the roles of each domain remain unclear.

RESULTS

In the present study, we focused on the genetic effects of different domains of qPE9-1 in the regulation of grain length and weight. We generated a series of transgenic plants expressing different truncated qPE9-1 proteins through constitutive expression and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 strategies. Phenotypic analysis indicated that the complete or long-tailed qPE9-1 contributed to the elongation of grains, while the GGL domain alone and short-tailed qPE9-1 led to short grains. The long C-terminus of qPE9-1 including two or three C-terminal von Willebrand factor type C domains effectively repressed the negative effects of the GGL domain on grain length and weight. qPE9-1-overexpressing lines in a Wuxianggeng 9 (carrying a qpe9-1 allele) background showed increased grain yield per plant, but lodging occurred in some years.

CONCLUSIONS

Manipulation of the C-terminal length of qPE9-1 through genetic engineering can be used to generate varieties with various grain lengths and weights according to different requirements in rice breeding. The genetic effects of qPE9-1/qpe9-1 are multidimensional, and breeders should take into account other factors including genetic backgrounds and planting conditions in the use of qPE9-1/qpe9-1.

Discovery of QTL Alleles for Grain Shape in the Japan-MAGIC Rice Population Using Haplotype Information

A majority of traits are determined by multiple quantitative trait loci (QTL) that can have pleiotropic effects. A multi-parent advanced generation inter-cross (MAGIC) population is well suited for genetically analyzing the effects of multiple QTL on traits of interest because it contains a higher number of QTL alleles than a biparental population. We previously produced the JAPAN-MAGIC (JAM) population, derived from eight rice (Oryza sativa L.) cultivars with high yield and biomass in Japan, and developed the method of genome-wide association study (GWAS) using haplotype information on the JAM lines. This method was effective for identifying major genes such as Waxy for eating quality and Sd1 for culm length. Here, we show that haplotype-based GWAS is also effective for the evaluation of multiple QTL with small effects on rice grain shape in the JAM lines. Although both the haplotype- and SNP-based GWAS identified multiple QTL for grain length and width, the sum of the estimated trait values of each allele for the QTL detected by haplotype-based GWAS had higher correlation with observed values than those detected by SNP-based GWAS, indicating high-accuracy QTL detection in the haplotype-based GWAS. Furthermore, the study revealed pleiotropic effects of some QTL regions in regulation of grain shape, suggesting that the haplotype-based GWAS using the JAM lines is an effective means to evaluate the main and side effects of haplotypes at each QTL. Information on the pleiotropic effects of haplotypes on various traits will be useful for designing ideal lines in a breeding program.

Seed coats as an alternative molecular factory: thinking outside the box

Seed coats as commodities. Seed coats play important roles in the protection of the embryo from biological attack and physical damage by the environment as well as dispersion strategies. A significant part of the energy devoted by the mother plant to seed production is channeled into the production of the cell layers and metabolites that surround the embryo. Nevertheless, in crop species these are often discarded post-harvest and are a wasted resource that could be processed to yield co-products. The production of novel compounds from existing metabolites is also a possibility. A number of macromolecules are already accumulated in these maternal layers that could be exploited in industrial applications either directly or via green chemistry, notably flavonoids, lignin, lignan, polysaccharides, lipid polyesters and waxes. Here, we summarize our knowledge of the in planta biosynthesis pathways of these macromolecules and their molecular regulation as well as potential applications. We also outline recent work aimed at providing further tools for increasing yields of existing molecules or the development of novel biotech approaches, as well as trial studies aimed at exploiting this underused resource.

Transient Heat Stress During Early Seed Development Primes Germination and Seedling Establishment in Rice

Rice yield is highly sensitive to increased temperature. Given the trend of increasing global temperatures, this sensitivity to higher temperatures poses a challenge for achieving global food security. Early seed development in rice is highly sensitive to unfavorable environmental conditions. Heat stress (HS) during this stage decreases seed size and fertility, thus reducing yield. Here, we explore the transgenerational phenotypic consequences of HS during early seed development on seed viability, germination, and establishment. To elucidate the impact of HS on the developmental events in post-zygotic rice seeds, we imposed moderate (35°C) and severe (39°C) HS treatments initiated 1 day after fertilization and maintained for 24, 48, or 72 h. The transient HS treatments altered the initiation of endosperm (ED) cellularization, seed size and/or the duration of spikelet ripening. Notably, seeds exposed to 24 and 48 h moderate HS exhibited higher germination rate compared to seeds derived from plants grown under control or severe HS. A short-term HS resulted in altered expression of Gibberellin (GA) and ABA biosynthesis genes during early seed development, and GA and ABA levels and starch content at maturity. The increased germination rate after 24 of moderate HS could be due to altered ABA sensitivity and/or increased starch level. Our findings on the impact of transient HS on hormone homeostasis provide an experimental framework to elucidate the underlying molecular and metabolic pathways.