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

The molecular mechanism of transcription factor regulation of grain size in rice

Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.

Rice grain size: current regulatory mechanisms and future perspectives

Rice is a staple food for over half of the world's population. To feed the growing population, molecular breeders aim to increase grain yield. Grain size is an important factor for crop productivity, and it has been extensively studied. However, molecular breeders face a major challenge in further improving crop productivity in terms of grain yield and quality. Grain size is a complex trait controlled by multiple genes. Over the past few decades, genetic studies have identified various gene families involved in grain size development. The list of molecular mechanisms, and key regulators involved in grain size development is constantly expanding, making it difficult to understand the main regulators that play crucial roles in grain development. In this review, we focus on the major regulators of grain size, including G-protein signaling, the mitogen-activated protein kinase (MAPK) pathway, transcriptional regulation, the ubiquitin-proteasome degradation (UPD) pathway, and phytohormone signaling. These molecular mechanisms directly or indirectly regulate grain size. We provided a comprehensive understanding of the genes involved in these mechanisms and cross discussions about how these mechanisms are interlinked. This review serves as a valuable resource for understanding the molecular mechanisms that govern grain development and can aid in the development of molecular breeding strategies.

Advances in auxin synthesis, transport, and signaling in rice: implications for stress resilience and crop improvement

Auxin, a crucial plant hormone, plays a pivotal role in regulating various aspects of rice growth and development, including cell elongation, root formation, and responses to environmental stimuli. Recent breakthroughs in auxin research have revealed novel regulatory mechanisms, such as the identification of auxin-related genes like DNR1 and OsARF18, which enhance rice nitrogen use efficience and resistance to glufosinate. Additionally, advancements in understanding auxin transport and signaling pathways have highlighted their potential in optimizing tillering, root architecture, and grain yield. This review examines these molecular mechanisms and their interactions with other hormones, emphasizing their integration into breeding programs for improved rice productivity. By synthesizing these findings, we provide a comprehensive overview of how auxin research informs strategies for developing rice varieties with enhanced adaptability and optimized growth, contributing to food security and sustainable agriculture.

The miR172a-SNB module orchestrates both induced and adult-plant resistance to multiple diseases via MYB30-mediated lignin accumulation in rice

Plants mount induced resistance and adult-plant resistance against different pathogens throughout the whole growth period. Rice production faces threats from multiple major diseases, including rice blast, sheath blight, and bacterial leaf blight. Here, we report that the miR172a-SNB-MYB30 module regulates both induced and adult-plant resistance to these three major diseases via lignification in rice. Mechanistically, pathogen infections induce the expression of miR172a, which downregulates the transcription factor SNB to release its suppression of MYB30, leading to an increase in lignin biosynthesis and disease resistance throughout the whole growth period. Moreover, expression levels of miR172a and MYB30 gradually increase and are consistently correlated with lignin contents and disease resistance during rice development, reaching a peak at full maturity, whereas SNB RNA levels are negatively correlated with lignin contents and disease resistance, indicating the involvement of the miR172a-SNB-MYB30 module in adult-plant resistance. The functional domain of SNB protein and its binding sites in the MYB30 promoter are highly conserved among more than 4000 rice accessions, while abnormal expression of miR172a, SNB, or MYB30 compromises yield traits, suggesting artificial selection of the miR172a-SNB-MYB30 module during rice domestication. Taken together, these results reveal a novel role for a conserved miRNA-regulated module that contributes significantly to induced and adult-plant resistance against multiple pathogens by increasing lignin accumulation, deepening our understanding of broad-spectrum resistance and adult-plant resistance.

How Helpful May Be a CRISPR/Cas-Based System for Food Traceability?

Genome editing (GE) technologies have the potential to completely transform breeding and biotechnology applied to crop species, contributing to the advancement of modern agriculture and influencing the market structure. To date, the GE-toolboxes include several distinct platforms able to induce site-specific and predetermined genomic modifications, introducing changes within the existing genetic blueprint of an organism. For these reasons, the GE-derived approaches are considered like new plant breeding methods, known also as New Breeding Techniques (NBTs). Particularly, the GE-based on CRISPR/Cas technology represents a considerable improvement forward biotech-related techniques, being highly sensitive, precise/accurate, and straightforward for targeted gene editing in a reliable and reproducible way, with numerous applications in food-related plants. Furthermore, numerous examples of CRISPR/Cas system exploitation for non-editing purposes, ranging from cell imaging to gene expression regulation and DNA assembly, are also increasing, together with recent engagements in target and multiple chemical detection. This manuscript aims, after providing a general overview, to focus attention on the main advances of CRISPR/Cas-based systems into new frontiers of non-editing, presenting and discussing the associated implications and their relative impacts on molecular traceability, an aspect closely related to food safety, which increasingly arouses general interest within public opinion and the scientific community.

Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops

BACKGROUND

Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far.

AIM OF REVIEW

This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.

Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh

Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice

Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC1F2 and BC1F2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality.

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

Nitrogen is a crucial element that impacts rice yields, and effective tillering is a significant agronomic characteristic that can influence rice yields. The way that reduced nitrogen affects effective tillering is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 469 germplasm varieties were used for a genome-wide association analysis aiming to detect quantitative trait loci (QTL) associated with effective tillering at low (60 kg/hm2) and high (180 kg/hm2) nitrogen levels. QTLs detected over multiple years or under different treatments were scrutinized in this study, and candidate genes were identified through haplotype analysis and spatio-temporal expression patterns. A total of seven genes (NAL1, OsCKX9, Os01g0690800, Os02g0550300, Os02g0550700, Os04g0615700, and Os04g06163000) were pinpointed in these QTL regions, and were considered the most likely candidate genes. These results provide favorable information for the use of auxiliary marker selection in controlling effective tillering in rice for improved yields.

2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice (Oryza sativa L.)

Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.

Regulatory mechanism of the miR172e-LbrAP2 module during the vegetative growth phase transition in Lilium

MAIN CONCLUSION

It was proved for the first time that the miR172e-LbrAP2 module regulated the vegetative growth phase transition in Lilium, which provided a new approach to shorten the juvenile stage of Lilium, improved the reproduction rate, and reduced the propagation cost of Lilium commercial bulbs. Lilium is an ornamental bulb plant that takes at least 3 years to cultivate into commercial seed bulbs under natural conditions. The aim of this study was to shorten the Lilium expansion cycle. In this study, the growth cycle of lily tubers induced by low temperature of 15 °C was significantly shorter than that of tubers grown at a conventional temperature. Quantitative real-time PCR analysis showed that the expression patterns of miR172e and LbrAP2 were negatively correlated. GUS histochemical staining confirmed that miR172e and LbrAP2 in tobacco leaves interacted with each other after co-transformation. The shear sites of miR172e and its target gene, LbrAP2, upon binding, were identified by RLM 5' RACE analysis. In addition, miR172e and LbrAP2 showed opposite expression patterns after the transformation of Arabidopsis. miR172e overexpression accelerated the transition from juvenile to adult plants, whereas LbrAP2 overexpression inhibited this process, thus indicating that miR172e negatively regulated the target gene LbrAP2. Upregulation of the transcription factor LbrAP2 delayed the phase transition of plants, whereas miR172 inhibited the transcriptional translation of LbrAP2, thereby accelerating the phase transition. Low-temperature treatment of Lilium bulbs can shorten Lilium development, which provides a new approach to accelerating Lilium commercial bulb breeding and reducing breeding costs.

Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley

Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.

Plant genome resequencing and population genomics: Current status and future prospects

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.

Genetically Modified Rice Is Associated with Hunger, Health, and Climate Resilience

While nearly one in nine people in the world deals with hunger, one in eight has obesity, and all face the threat of climate change. The production of rice, an important cereal crop and staple food for most of the world's population, faces challenges due to climate change, the increasing global population, and the simultaneous prevalence of hunger and obesity worldwide. These issues could be addressed at least in part by genetically modified rice. Genetic engineering has greatly developed over the century. Genetically modified rice has been approved by the ISAAA's GM approval database as safe for human consumption. The aim behind the development of this rice is to improve the crop yield, nutritional value, and food safety of rice grains. This review article provides a summary of the research data on genetically modified rice and its potential role in improving the double burden of malnutrition, primarily through increasing nutritional quality as well as grain size and yield. It also reviews the potential health benefits of certain bioactive components generated in genetically modified rice. Furthermore, this article discusses potential solutions to these challenges, including the use of genetically modified crops and the identification of quantitative trait loci involved in grain weight and nutritional quality. Specifically, a quantitative trait locus called grain weight on chromosome 6 has been identified, which was amplified by the Kasa allele, resulting in a substantial increase in grain weight and brown grain. An overexpressing a specific gene in rice, Oryza sativa plasma membrane H+-ATPase1, was observed to improve the absorption and assimilation of ammonium in the roots, as well as enhance stomatal opening and photosynthesis rate in the leaves under light exposure. Cloning research has also enabled the identification of several underlying quantitative trait loci involved in grain weight and nutritional quality. Finally, this article discusses the increasing threats of climate change such as methane-nitrous oxide emissions and global warming, and how they may be significantly improved by genetically modified rice through modifying a water-management technique. Taken together, this comprehensive review will be of particular importance to the field of bioactive components of cereal grains and food industries trying to produce high-quality functional cereal foods through genetic engineering.

Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications

Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies.

Candidate genes affecting stomatal density in rice (Oryza sativa L.) identified by genome-wide association

Stomata regulate photosynthesis and water loss. They have been an active subject of research for centuries, but our knowledge of the genetic components that regulate stomatal development in crops remains very limited in comparison to the model plant Arabidopsis thaliana. Leaf stomatal density was found to vary by over 2.5-fold across a panel of 235 rice accessions. Using GWAS, we successfully identified five different QTLs associated with stomatal density on chromosomes 2, 3, 9, and 12. Forty-two genes were identified within the haplotype blocks corresponding to these QTLs. Of these, nine genes contained haplotypes that were associated with different stomatal densities. These include a gene encoding a trehalose-6-phosphate synthase, an enzyme that has previously been associated with altered stomatal density in Arabidopsis, and genes encoding a B-BOX zinc finger family protein, a leucine-rich repeat family protein, and the 40 S ribosomal protein S3a, none of which have previously been linked to stomatal traits. We investigated further and show that a closely related B-BOX protein regulates stomatal development in Arabidopsis. The results of this study provide information on genetic associations with stomatal density in rice. The QTLs and candidate genes may be useful in future breeding programs for low or high stomatal density and, consequently, improved photosynthetic capacity, water use efficiency, or drought tolerance.

Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review

Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.

Natural variation of Alfin-like family affects seed size and drought tolerance in rice

The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.

CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.

Identification and Investigation of the Genetic Variations and Candidate Genes Responsible for Seed Weight via GWAS in Paper Mulberry

Seeds directly determine the survival and population size of woody plants, but the genetic basis of seed weight in woody plants remain poorly explored. To identify genetic variations and candidate genes responsible for seed weight in natural woody populations, we investigated the hundred-seed weight of 198 paper mulberry individuals from different areas. Our results showed that the hundred-seed weight of paper mulberry was significantly associated with the bioclimatic variables of sampling sites, which increased from south to north along the latitudinal-temperature gradient. Using 2,414,978 high-quality SNPs from re-sequencing data, the genome-wide association analysis of the hundred-seed weight was performed under three models, which identified 148, 19 and 12 associated genes, respectively. Among them, 25 candidate genes were directly hit by the significant SNPs, including the WRKY transcription factor, fatty acid desaturase, F-box protein, etc. Most importantly, we identified three crucial genetic variations in the coding regions of candidate genes (Bp02g2123, Bp01g3291 and Bp10g1642), and significant differences in the hundred-seed weight were detected among the individuals carrying different genotypes. Further analysis revealed that Bp02g2123 encoding a fatty acid desaturase (FAD) might be a key factor affecting the seed weight and local climate adaptation of woody plants. Furthermore, the genome-wide investigation and expression analysis of FAD genes were performed, and the results suggested that BpFADs widely expressed in various tissues and responded to multiple phytohormone and stress treatments. Overall, our study identifies valuable genetic variations and candidate genes, and provides a better understanding of the genetic basis of seed weight in woody plants.

Molecular Events of Rice AP2/ERF Transcription Factors

APETALA2/ethylene response factor (AP2/ERF) is widely found in the plant kingdom and plays crucial roles in transcriptional regulation and defense response of plant growth and development. Based on the research progress related to AP2/ERF genes, this paper focuses on the classification and structural features of AP2/ERF transcription factors, reviews the roles of rice AP2/ERF genes in the regulation of growth, development and stress responses, and discusses rice breeding potential and challenges. Taken together; studies of rice AP2/ERF genes may help to elucidate and enrich the multiple molecular mechanisms of how AP2/ERF genes regulate spikelet determinacy and floral organ development, flowering time, grain size and quality, embryogenesis, root development, hormone balance, nutrient use efficiency, and biotic and abiotic response processes. This will contribute to breeding excellent rice varieties with high yield and high resistance in a green, organic manner.

CRISPR/Cas9 Technology and Its Utility for Crop Improvement

The rapid growth of the global population has resulted in a considerable increase in the demand for food crops. However, traditional crop breeding methods will not be able to satisfy the worldwide demand for food in the future. New gene-editing technologies, the most widely used of which is CRISPR/Cas9, may enable the rapid improvement of crop traits. Specifically, CRISPR/Cas9 genome-editing technology involves the use of a guide RNA and a Cas9 protein that can cleave the genome at specific loci. Due to its simplicity and efficiency, the CRISPR/Cas9 system has rapidly become the most widely used tool for editing animal and plant genomes. It is ideal for modifying the traits of many plants, including food crops, and for creating new germplasm materials. In this review, the development of the CRISPR/Cas9 system, the underlying mechanism, and examples of its use for editing genes in important crops are discussed. Furthermore, certain limitations of the CRISPR/Cas9 system and potential solutions are described. This article will provide researchers with important information regarding the use of CRISPR/Cas9 gene-editing technology for crop improvement, plant breeding, and gene functional analyses.

Genetic control of grain appearance quality in rice

Grain appearance, one of the key determinants of rice quality, reflects the ability to attract consumers, and is characterized by four major properties: grain shape, chalkiness, transparency, and color. Mining of valuable genes, genetic mechanisms, and breeding cultivars with improved grain appearance are essential research areas in rice biology. However, grain appearance is a complex and comprehensive trait, making it challenging to understand the molecular details, and therefore, achieve precise improvement. This review highlights the current findings of grain appearance control, including a detailed description of the key genes involved in the formation of grain appearance, and the major environmental factors affecting chalkiness. We also discuss the integration of current knowledge on valuable genes to enable accurate breeding strategies for generation of rice grains with superior appearance quality.

A superior allele of the wheat gene TaGL3.3-5B, selected in the breeding process, contributes to seed size and weight

A superior allele of wheat gene TaGL3.3-5B was identified and could be used in marker-assisted breeding in wheat. Identifying the main genes which mainly regulate the yield-associated traits can significantly increase the wheat production. In this study, gene TaGL3.3 was cloned from common wheat according to the sequence of OsPPKL3. A SNP in the 8th exon of TaGL3.3-5B, T/C in coding sequence (CDS), which resulted in an amino acid change (Val/Ala), was identified between the low 1000-kernel weight (TKW) wheat Chinese Spring and the high TKW wheat Xinong 817 (817). Subsequently, association analysis in the mini-core collection (MCC) and the recombinant inbred lines (RIL) revealed that the allele TaGL3.3-5B-C (from 817) was significantly correlated with higher TKW. The high frequency of TaGL3.3-5B-C in the Chinese modern wheat cultivars indicated that it was selected positively in wheat breeding programs. The overexpression of TaGL3.3-5B-C in Arabidopsis resulted in shorter pods and longer grains than those of wild-type counterparts. Additionally, TaGL3.3 expressed a tissue-specific pattern in wheat as revealed by qRT-PCR. We also found that 817 showed higher expression of TaGL3.3 than that in Chinese Spring (CS) during the seed development. These results demonstrate that TaGL3.3 plays an important role in the formation of seed size and weight. Allele TaGL3.3-5B-C is associated with larger and heavier grains that are beneficial to wheat yield improvement.

Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops

In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.

Dissection of the Genetic Basis of Yield Traits in Line per se and Testcross Populations and Identification of Candidate Genes for Hybrid Performance in Maize

Dissecting the genetic basis of yield traits in hybrid populations and identifying the candidate genes are important for molecular crop breeding. In this study, a BC1F3:4 population, the line per se (LPS) population, was constructed by using elite inbred lines Zheng58 and PH4CV as the parental lines. The population was genotyped with 55,000 SNPs and testcrossed to Chang7-2 and PH6WC (two testers) to construct two testcross (TC) populations. The three populations were evaluated for hundred kernel weight (HKW) and yield per plant (YPP) in multiple environments. Marker-trait association analysis (MTA) identified 24 to 151 significant SNPs in the three populations. Comparison of the significant SNPs identified common and specific quantitative trait locus/loci (QTL) in the LPS and TC populations. Genetic feature analysis of these significant SNPs proved that these SNPs were associated with the tested traits and could be used to predict trait performance of both LPS and TC populations. RNA-seq analysis was performed using maize hybrid varieties and their parental lines, and differentially expressed genes (DEGs) between hybrid varieties and parental lines were identified. Comparison of the chromosome positions of DEGs with those of significant SNPs detected in the TC population identified potential candidate genes that might be related to hybrid performance. Combining RNA-seq analysis and MTA results identified candidate genes for hybrid performance, providing information that could be useful for maize hybrid breeding.

DTH8 overexpression induces early flowering, boosts yield, and improves stress recovery in rice cv IR64

Rice yield and heading date are the two discrete traits controlled by quantitative trait loci (QTLs). Both traits are influenced by the genetic make-up of the plant as well as the environmental factors where it thrives. Drought and salinity adversely affect crop productivity in many parts of the world. Tolerance to these stresses is multigenic and complex in nature. In this study, we have characterized a QTL, DTH8 (days to heading) from Oryza sativa L. cv IR64 that encodes a putative HAP3/NF-YB/CBF subunit of CCAAT-box binding protein (HAP complex). We demonstrate DTH8 to be positively influencing the yield, heading date, and stress tolerance in IR64. DTH8 up-regulates the transcription of RFT1, Hd3a, GHD7, MOC1, and RCN1 in IR64 at the pre-flowering stage and plays a role in early flowering, increased number of tillers, enhanced panicle branching, and improved tolerance towards drought and salinity stress at the reproductive stage. The presence of DTH8 binding elements (CCAAT) in the promoter regions of all of these genes, predicted by in silico analysis of the promoter region, indicates the regulation of their expression by DTH8. In addition, DTH8 overexpressing transgenic lines showed favorable physiological parameters causing less yield penalty under stress than the WT plants. Taken together, DTH8 is a positive regulator of the network of genes related to early flowering/heading, higher yield, as well as salinity and drought stress tolerance, thus, enabling the crops to adapt to a wide range of climatic conditions.

OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development

Stem cell homeostasis by the WUSCHEL-CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnormality and defects in developmental progression. The size of the shoot apical meristem (SAM) in 25-day OsbZIP47KD plants was increased as compared to the wild-type (WT). Inflorescence of KD plants showed reduced rachis length, number of primary branches, and spikelets. Florets had defects in the second and third whorl organs and increased organ number. OsbZIP47KD SAM and panicles had abnormal expression for CLAVATA peptide-like signaling genes, such as FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway genes, such as cytokinin (CK) ISOPENTEYLTRANSFERASE1 (OsIPT1), ISOPENTEYLTRANSFERASE 8 (OsIPT8), auxin biosynthesis OsYUCCA6, OsYUCCA7 and gibberellic acid (GA) biosynthesis genes, such as GRAIN NUMBER PER PANICLE1 (GNP1/OsGA20OX1) and SHORTENED BASAL INTERNODE (SBI/OsGA2ox4). The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF (DL) relate to the second and third whorl floret phenotypes in OsbZIP47KD. Protein interaction assays showed OsbZIP47 partnerships with RICE HOMEOBOX1 (OSH1), RICE FLORICULA/LEAFY (RFL), and OsMADS1 transcription factors. The meta-analysis of KD panicle transcriptomes in OsbZIP47KD, OsMADS1KD, and RFLKD transgenics, combined with global OSH1 binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1, and RFL. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding affinity to a cis element in FCP1, a target locus. Taken together, we provide insights on OsbZIP47 roles in SAM development, inflorescence branching, and floret development.

CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull

Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice.

Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population

A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03045-7.

Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice

BACKGROUND

Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production.

RESULTS

Here, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance.

CONCLUSIONS

This is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.

Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

BACKGROUND

Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape.

RESULTS

Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided.

CONCLUSIONS

Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.

Modification of cereal plant architecture by genome editing to improve yields

KEY MESSAGE

We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.

Hotter, drier, CRISPR: the latest edit on climate change

Integrating CRISPR/Cas9 genome editing into modern breeding programs for crop improvement in cereals. Global climate trends in many agricultural regions have been rapidly changing over the past decades, and major advances in global food systems are required to ensure food security in the face of these emerging challenges. With increasing climate instability due to warmer temperatures and rising CO₂ levels, the productivity of global agriculture will continue to be negatively impacted. To combat these growing concerns, creative approaches will be required, utilising all the tools available to produce more robust and tolerant crops with increased quality and yields under more extreme conditions. The integration of genome editing and transgenics into current breeding strategies is one promising solution to accelerate genetic gains through targeted genetic modifications, producing crops that can overcome the shifting climate realities. This review focuses on how revolutionary genome editing tools can be directly implemented into breeding programs for cereal crop improvement to rapidly counteract many of the issues affecting agriculture production in the years to come.

Identification of QTL for barley grain size

Background

Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size.

Methods

Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size.

Results

A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.

The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce

Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks that operate during seed development remain unclear in lettuce. Here, we identified a lettuce AP2 (LsAP2) gene that was highly expressed during the early stages of seed development. LsAP2 knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function of LsAP2. Compared with the wild type, the seeds of Lsap2 mutant plants were longer and narrower, and developed an extended tip at the seed top. After further investigating the structural characteristics of the seeds of Lsap2 mutant plants, we proposed a new function of LsAP2 in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression of LsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.

APETALA2 functions as a temporal factor together with BLADE-ON-PETIOLE2 and MADS29 to control flower and grain development in barley

Cereal grain develops from fertilised florets. Alterations in floret and grain development greatly influence grain yield and quality. Despite this, little is known about the underlying genetic control of these processes, especially in key temperate cereals such as barley and wheat. Using a combination of near-isogenic mutant comparisons, gene editing and genetic analyses, we reveal that HvAPETALA2 (HvAP2) controls floret organ identity, floret boundaries, and maternal tissue differentiation and elimination during grain development. These new roles of HvAP2 correlate with changes in grain size and HvAP2-dependent expression of specific HvMADS-box genes, including the B-sister gene, HvMADS29. Consistent with this, gene editing demonstrates that HvMADS29 shares roles with HvAP2 in maternal tissue differentiation. We also discovered that a gain-of-function HvAP2 allele masks changes in floret organ identity and grain size due to loss of barley LAXATUM.A/BLADE-ON-PETIOLE2 (HvBOP2) gene function. Taken together, we reveal novel pleiotropic roles and regulatory interactions for an AP2-like gene controlling floret and grain development in a temperate cereal.

Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice

A minor QTL for grain weight in rice, qTGW1.2b, was fine-mapped. Its casual gene OsVQ4 was confirmed through CRISPR/Cas9-targeted mutagenesis, exhibiting an effect that was larger than the original QTL effect. The CRISPR/Cas system exhibits a great potential for rice improvement, but the application was severely hindered due to insufficient target genes, especial the lack of validated genes underlying quantitative trait loci having small effects. In this study, a minor QTL for grain weight, qTGW1.2b, was fine-mapped into a 44.0 kb region using seven sets of near isogenic lines (NILs) developed from the indica rice cross (Zhenshan 97)³/Milyang 46, followed by validation of the causal gene using CRISPR/Cas9-targeted mutagenesis. In the NIL populations, 1000-grain weight of the Zhenshan 97 homozygous lines decreased by 0.9-2.0% compared with the Milyang 46 homozygous lines. A gene encoding VQ-motif protein, OsVQ4, was identified as the candidate gene based on parental sequence differences. The effect of OsVQ4 was confirmed by creating CRISPR/Cas9 knockout lines, whose 1000-grain weight decreased by 2.8-9.8% compared with the wild-type transgenic line and the recipient. These results indicate that applying genome editing system could create novel alleles with large phenotypic variation at minor QTLs, which is an effective way to validate causal genes of minor QTLs. Our study establishes a strategy for cloning minor QTLs, which could also be used to identify a large number of potential target genes for the application of CRISPR/Cas system.

Genome-Wide Association Study of Root System Development at Seedling Stage in Rice

Root network structure plays a crucial role in growth and development processes in rice. Longer, more branched root structures help plants to assimilate water and nutrition from soil, support robust plant growth, and improve resilience to stresses such as disease. Understanding the molecular basis of root development through screening of root-related traits in rice germplasms is critical to future rice breeding programs. This study used a small germplasm collection of 137 rice varieties chosen from the Korean rice core set (KRICE_CORE) to identify loci linked to root development. Two million high-quality single nucleotide polymorphisms (SNPs) were used as the genotype, with maximum root length (MRL) and total root weight (TRW) in seedlings used as the phenotype. Genome-wide association study (GWAS) combined with Principal Components Analysis (PCA) and Kinship matrix analysis identified four quantitative trait loci (QTLs) on chromosomes 3, 6, and 8. Two QTLs were linked to MRL and two were related to TRW. Analysis of Linkage Disequilibrium (LD) decay identified a 230 kb exploratory range for detection of candidate root-related genes. Candidates were filtered using RNA-seq data, gene annotations, and quantitative real-time PCR (qRT-PCR), and five previously characterized genes related to root development were identified, as well as four novel candidate genes. Promoter analysis of candidate genes showed that LOC_Os03g08880 and LOC_Os06g13060 contained SNPs with the potential to impact gene expression in root-related promoter motifs. Haplotype analysis of candidate genes revealed diverse haplotypes that were significantly associated with phenotypic variation. Taken together, these results indicate that LOC_Os03g08880 and LOC_Os06g13060 are strong candidate genes for root development functions. The significant haplotypes identified in this study will be beneficial in future breeding programs for root improvement.

Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping

The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.

Advances in genome-wide association studies of complex traits in rice

Genome-wide association studies (GWAS), genetic surveys of the whole genome to detect variants associated with a trait in natural populations, are a powerful approach for dissecting complex traits. This genetic mapping approach has been applied in rice over the last 10 years. During the last decade, GWAS was used to identify the loci underlying tens of rice traits, and several important genes were detected in GWAS and further confirmed in follow-up functional experiments. In this review, we present an overview of the whole process in a typical GWAS, including population design, genotyping, phenotyping and analysis methods. Recent advances in rice GWAS are also provided, including several examples of the functional characterization of candidate genes. The possible breakthroughs of rice GWAS in the next decade are discussed with regard to their application in breeding, the consideration of epistatic interactions and in-depth functional annotations of DNA elements and genetic variants throughout the rice genome.

Marker-assisted selection for grain number and yield-related traits of rice (Oryza sativa L.)

Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

Rice grain size plays a crucial role in determining grain quality and yield. In this study, two multiparent advanced generation intercross (MAGIC) populations, DC1 and BIM, were evaluated for grain size across three environments and genotyped with 55K array-based SNP detection and genotype-by-sequencing (GBS), respectively, to identify QTLs and SNPs associated with grain length, grain width, grain length-width ratio, grain thickness, and thousand grain weight. A total of 18 QTLs were identified for the five grain size-related traits and explained 6.43-63.35% of the total phenotypic variance. Twelve of these QTLs colocalized with the cloned genes, GS3, GW5/qSW5, GW7/GL7/SLG7, and GW8/OsSPL16, of which the first two genes showed the strongest effect for grain length and grain width, respectively. Four potential new genes were also identified from the QTLs, which exhibited both genetic background independency and environment stability and could be validated in future studies. Moreover, the significant SNP markers identified are valuable for direct utilization in marker-assisted breeding to improve rice grain size.

Identification of QTL TGW12 responsible for grain weight in rice based on recombinant inbred line population crossed by wild rice (Oryza minuta) introgression line K1561 and indica rice G1025

Background

Limited genetic resource in the cultivated rice may hinder further yield improvement. Some valuable genes that contribute to rice yield may be lost or lacked in the cultivated rice. Identification of the quantitative trait locus (QTL) for yield-related traits such as thousand-grain weight (TGW) from wild rice speices is desired for rice yield improvement.

Results

In this study, sixteen TGW QTL were identified from a recombinant inbred line (RIL) population derived from the cross between the introgression line K1561 of Oryza minuta and the rice cultivar G1025. TGW12, One of most effective QTL was mapped to the region of 204.12 kb between the marker 2,768,345 and marker 2,853,491 of the specific locus amplified fragment (SLAF). The origin of TGW12 was tested using three markers nearby or within the TGW12 region, but not clarified yet. Our data indicated thirty-two open reading fragments (ORFs) were present in the region. RT-PCR analysis and sequence alignment showed that the coding domain sequences of ORF12, one MADS-box gene, in G1025 and K1561 were different due to alternative slicing, which caused premature transcription termination. The MADS-box gene was considered as a candidate of TGW12.

Conclusion

The effective QTL, TGW12, was mapped to a segment of 204.12 kb using RILs population and a MADS-box gene was identified among several candidate genes in the segment. The region of TGW12 should be further narrowed and creation of transgenic lines will reveal the gene function. TGW12 could be applied for improvement of TGW in breeding program.

Revolutions in agriculture chart a course for targeted breeding of old and new crops

The dominance of the major crops that feed humans and their livestock arose from agricultural revolutions that increased productivity and adapted plants to large-scale farming practices. Two hormone systems that universally control flowering and plant architecture, florigen and gibberellin, were the source of multiple revolutions that modified reproductive transitions and proportional growth among plant parts. Although step changes based on serendipitous mutations in these hormone systems laid the foundation, genetic and agronomic tuning were required for broad agricultural benefits. We propose that generating targeted genetic variation in core components of both systems would elicit a wider range of phenotypic variation. Incorporating this enhanced diversity into breeding programs of conventional and underutilized crops could help to meet the future needs of the human diet and promote sustainable agriculture.