Genome-Wide Association Study on Root System Architecture and Identification of Candidate Genes in Wheat (Triticum aestivum L.)

The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of −log₁₀ (p-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes, TraesCS2A01G516200 and TraesCS7B01G036900, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat.     

Identification of Candidate Genes for Root Traits Using Genotype–Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat (Triticum aestivum L.)

Global wheat (Triticum aestivum L.) production is constrained by different biotic and abiotic stresses, which are increasing with climate change. An improved root system is essential for adaptability and sustainable wheat production. In this study, 10 pairs of near-isogenic lines (NILs)—targeting four genomic regions (GRs) on chromosome arms 4BS, 4BL, 4AS, and 7AL of hexaploid wheat—were used to phenotype root traits in a semi-hydroponic system. Seven of the 10 NIL pairs significantly differed between their isolines for 11 root traits. The NIL pairs targeting qDSI.4B.1 GR varied the most, followed by the NIL pair targeting qDT.4A.1 and QHtscc.ksu-7A GRs. For pairs 5–7 targeting qDT.4A.1 GR, pair 6 significantly differed in the most root traits. Of the 4 NIL pairs targeting qDSI.4B.1 GR, pairs 2 and 4 significantly differed in 3 and 4 root traits, respectively. Pairs 9 and 10 targeting QHtscc.ksu-7A GR significantly differed in 1 and 4 root traits, respectively. Using the wheat 90K Illumina iSelect array, we identified 15 putative candidate genes associated with different root traits in the contrasting isolines, in which two UDP-glycosyltransferase (UGT)-encoding genes, TraesCS4A02G185300 and TraesCS4A02G442700, and a leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene, TraesCS4A02G330900, also showed important functions for root trait control in other crops. This study characterized, for the first time, that these GRs control root traits in wheat, and identified candidate genes, although the candidate genes will need further confirmation and validation for marker-assisted wheat breeding.     

The Role of Hydrogen Sulfide in Plant Roots during Development and in Response to Abiotic Stress

Hydrogen sulfide (H₂S) is regarded as a “New Warrior” for managing plant stress. It also plays an important role in plant growth and development. The regulation of root system architecture (RSA) by H₂S has been widely recognized. Plants are dependent on the RSA to meet their water and nutritional requirements. They are also partially dependent on the RSA for adapting to environment change. Therefore, a good understanding of how H₂S affects the RSA could lead to improvements in both crop function and resistance to environmental change. In this review, we summarized the regulating effects of H₂S on the RSA in terms of primary root growth, lateral and adventitious root formation, root hair development, and the formation of nodules. We also discussed the genes involved in the regulation of the RSA by H₂S, and the relationships with other signal pathways. In addition, we discussed how H₂S regulates root growth in response to abiotic stress. This review could provide a comprehensive understanding of the role of H₂S in roots during development and under abiotic stress.     

The Role of Strigolactones in the Regulation of Root System Architecture in Grapevine (Vitis vinifera L.) in Response to Root-Restriction Cultivation

This study investigated the effects of root-restriction cultivation on the root architecture, endogenous strigolactone (SL) content, and SL-related genes expression in grapevine (Vitis vinifera L.). In addition, we clarified the effects of synthetic SL analog GR24 application on grapevine roots to explore the role of SLs in their development. The results showed that the root architecture changed significantly under root-restriction cultivation. At 40 days after transplantation (DAT), the contents of two types of SLs in roots under root restriction were both significantly lower than that in roots of the control. SL content was significantly positively correlated with the expression levels of VvCCD8 and VvD27, indicating that they play vital roles in SLs synthesis. After GR24 treatment for 20 days, the root length was significantly shorter than in the control. A low concentration (0.1 μM) of GR24 significantly reduced the root diameter and increased the fine-root density, while a high concentration (10 μM) of GR24 significantly reduced the lateral root (LR) length and increased the LR density. Concomitantly, GR24 (0.1 μM) reduced endogenous SL content. After GR24 treatment for 5 days, the total content of two tested SLs was highly positively correlated with the expression levels of VvDAD2, whereas it was highly negatively correlated with VvSMAXL4 at 20 days after GR24 treatment. This study helps to clarify the internal mechanism of root-restriction cultivation affecting the changes in grapevine root architecture, as well as further explore the important role of SLs in the growth of grapevine roots in response to root-restriction treatment.     

Differences Among Rice Cultivars in Root Exudation, Methane Oxidation, and Populations of Methanogenic and Methanotrophic Bacteria in Relation to Methane Emission

Greenhouse experiments were conducted under subtropical conditions to understand the mechanism of rice cultivar differences in methane (CH₄) emission. Three rice cultivars were studied. Differences in CH₄ emission rates among the three rice cultivars became evident in the middle and late growth stages. Rice root exudates per plant measured as total released C were significantly different among rice cultivars. The effect of root exudates on CH₄ production in soil slurry differed accordingly. The amount of root exudates was not significantly different among rice cultivars when computed on a dry matter basis, indicating that it is positively correlated to root dry matter production. The root CH₄-oxidizing activity differed among rice cultivars. IR65598 had a higher oxidative activity than IR72 and Chiyonishiki. Root air space was not significantly different among rice cultivars at the late growth stage, indicating that it is probably not a factor contributing to cultivar differences in CH₄ emission. The population level of methanogenic bacteria differed significantly in soil grown to different rice cultivars, but not in roots, at booting stage and ripening stage. Methanotrophic bacteria population differed significantly in roots among rice cultivars at ripening. Rice cultivars with few unproductive tillers, small root system, high root oxidative activity, and high harvest index are ideal for mitigating CH₄ emission in rice fields.     

Discovery of Genomic Regions and Candidate Genes Controlling Root Development Using a Recombinant Inbred Line Population in Rapeseed (Brassica napus L.)

Marker-assisted selection enables breeders to quickly select excellent root architectural variations, which play an essential role in plant productivity. Here, ten root-related and shoot biomass traits of a new F₆ recombinant inbred line (RIL) population were investigated under hydroponics and resulted in high heritabilities from 0.61 to 0.83. A high-density linkage map of the RIL population was constructed using a Brassica napus 50k Illumina single nucleotide polymorphism (SNP) array. A total of 86 quantitative trait loci (QTLs) explaining 4.16–14.1% of the phenotypic variances were detected and integrated into eight stable QTL clusters, which were repeatedly detected in different experiments. The codominant markers were developed to be tightly linked with three major QTL clusters, qcA09-2, qcC08-2, and qcC08-3, which controlled both root-related and shoot biomass traits and had phenotypic contributions greater than 10%. Among these, qcA09-2, renamed RT.A09, was further fine-mapped to a 129-kb interval with 19 annotated genes in the B. napus reference genome. By integrating the results of real-time PCR and comparative sequencing, five genes with expression differences and/or amino acid differences were identified as important candidate genes for RT.A09. Our findings laid the foundation for revealing the molecular mechanism of root development and developed valuable markers for root genetic improvement in rapeseed.     

Identification of a Major QTL and Validation of Related Genes for Tiller Angle in Rice Based on QTL Analysis

An ideal plant architecture is an important condition to achieve high crop yields. The tiller angle is an important and complex polygenic trait of rice (Oryza sativa L.) plant architecture. Therefore, the discovery and identification of tiller angle-related genes can aid in the improvement of crop architecture and yield. In the present study, 222 SSR markers were used to establish a high-density genetic map of rice doubled haploid population, and a total of 8 quantitative trait loci (QTLs) were detected based on the phenotypic data of the tiller angle and tiller crown width over 2 years. Among them, four QTLs (qTA9, qCW9, qTA9-1, and qCW9-1) were overlapped at marker interval RM6235–RM24288 on chromosome 9 with a large effect value regarded as a stable major QTL. The selected promising related genes were further identified by relative gene expression analysis, which gives us a basis for the future cloning of these genes. Finally, OsSAURq9, which belongs to the SMALL AUXIN UP RNA (SAUR), an auxin-responsive protein family, was selected as a target gene. Overall, this work will help broaden our knowledge of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.     

Effect of green manuring with Sesbania aculeata and nitrogen fertilization on the performance of direct-seeded flood-prone lowland rice

Green manuring of rice with dhaincha (Sesbania aculeata) is widely practised under irrigated puddle-transplanted conditions. In flood-prone lowlands, the rice is established through direct seeding early in the season and flooding occurs after 1–2 months of crop growth following regular rains. The low yields are due to poor crop stands and difficulty in nitrogen management under higher depths of water. The effect of green manuring with dhaincha intercropped with direct-seeded rice vis-à-vis the conventional practice of incorporating pure dhaincha before transplanting was investigated under flood-prone lowland conditions (up to 50–80 cm water depth) at Cuttack, India. Treatment variables studied in different years (1992, 1994 and 1995) were: rice varieties of different plant heights, crop establishment through direct seeding and transplanting, varying length of periods before dhaincha incorporation, and urea N fertilizer levels. Dhaincha accumulated 80–86 kg N ha^-1 in pure stand and 58–79 kg N ha^-1 when intercropped with direct-seeded rice in alternate rows at 50 days of growth. The growth of rice improved after dhaincha was uprooted manually and buried in situ between the rice rows when water depth was 10–20 cm in the field. The panicle number was lower but the panicle weight was higher with dhaincha green manuring than with recommended level of 40 kg N ha^-1 applied as urea. The grain yield was significantly higher with direct seeding than with transplanting due to high water levels (>60 cm) immediately after transplanting. Dhaincha manuring was at par with 40 kg N ha^-1 as urea in increasing the yield of direct-seeded and transplanted crops. The highest yield of direct-seeded crop was obtained when 20 kg N ha^-1 was applied at sowing and dhaincha was incorporated at 50 days of growth. The results indicate that green manuring of direct-seeded rice with intercropped dhaincha is beneficial for substituting urea fertilizer up to 40 kg N ha^-1 and augmenting crop productivity under flood-prone lowland conditions.     

Serine Hydroxymethyltransferase 1 Is Essential for Primary-Root Growth at Low-Sucrose Conditions

Plant roots are essential organs for absorbing nutrients from the soil or medium. Sucrose functions as a vital carbon source in root development, and sucrose starvation interferes with the redox state of plant cells. However, the mechanism of root growth at sucrose starvation remains unclear. Here, we report that SHMT1 (serine hydroxymethyltransferase 1) plays a crucial role in primary-root growth. SHMT1 mutation caused decreased sugar levels, excessive H₂O₂ accumulation, and severe root-growth arrest at sucrose-free conditions, whereas plants with SHMT1 overexpression had increased sugar and decreased H₂O₂ levels, and longer primary roots. Sucrose supply fully restored root growth of shm1-2, but CO₂ alone could not, and SHMT1 is much more stable in roots than shoots at sucrose conditions, suggesting that SHMT1 accumulation in roots is critical for sucrose accumulation and root growth. Further ROS scavenging by GSH application or ROS synthesis inhibition by apocynin application or RBOHD mutation reduced H₂O₂ levels and partially restored the root-growth arrest phenotype of shm1-2 at low-sucrose conditions, suggesting that SHMT1 modulates root growth via sucrose-mediated ROS accumulation. Our findings demonstrated the role of SHMT1 in primary-root growth by regulating sucrose accumulation and ROS homeostasis in roots.     

Exogenous SA Affects Rice Seed Germination under Salt Stress by Regulating Na+/K+ Balance and Endogenous GAs and ABA Homeostasis

Salinity reduces agricultural productivity majorly by inhibiting seed germination. Exogenous salicylic acid (SA) can prevent the harm caused to rice by salinity, but the mechanisms by which it promotes rice seed germination under salt stress are unclear. In this study, the inhibition of germination in salt-sensitive Nipponbare under salt stress was greater than that in salt-tolerant Huaidao 5. Treatment with exogenous SA significantly improved germination of Nipponbare, but had little effect on Huaidao 5. The effects of exogenous SA on ion balance, metabolism of reactive oxygen species (ROS), hormone homeostasis, starch hydrolysis, and other physiological processes involved in seed germination of rice under salt stress were investigated. Under salt stress, Na⁺ content and the Na⁺/K⁺ ratio in rice seeds increased sharply. Seeds were subjected to ion pressure, which led to massive accumulation of H₂O₂, O₂⁻, and malonaldehyde (MDA); imbalanced endogenous hormone homeostasis; decreased gibberellic acid (GA1 and GA4) content; increased abscisic acid (ABA) content; inhibition of α-amylase (EC 3.2.1.1) activity; and slowed starch hydrolysis rate, all which eventually led to the inhibition of the germination of rice seeds. Exogenous SA could effectively enhance the expression of OsHKT1;1, OsHKT1;5, OsHKT2;1 and OsSOS1 to reduce the absorption of Na+ by seeds; reduce the Na⁺/K⁺ ratio; improve the activities of SOD, POD, and CAT; reduce the accumulation of H₂O₂, O₂⁻, and MDA; enhance the expression of the GA biosynthetic genes OsGA20ox1 and OsGA3ox2; inhibit the expression of the ABA biosynthetic gene OsNCED5; increase GA1 and GA4 content; reduce ABA content; improve α-amylase activity, and increase the content of soluble sugars. In summary, exogenous SA can alleviate ion toxicity by reducing Na⁺ content, thereby helping to maintain ROS and hormone homeostasis, promote starch hydrolysis, and provide sufficient energy for seed germination, all of which ultimately improves rice seed germination under salt stress. This study presents a feasible means for improving the germination of direct-seeded rice in saline soil.     

Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.     

Simultaneous Improvement of Grain Yield and Quality through Manipulating Two Type C G Protein Gamma Subunits in Rice

Heterotrimeric G protein signaling is an evolutionarily conserved mechanism in diverse organisms that mediates intracellular responses to external stimuli. In rice, the G proteins are involved in the regulation of multiple important agronomic traits. In this paper, we present our finding that two type C G protein gamma subunits, DEP1 and GS3, antagonistically regulated grain yield and grain quality. The DEP1 gene editing we conducted, significantly increased the grain number per panicle but had a negative impact on taste value, texture properties, and chalkiness-related traits. The GS3 gene editing decreased grain number per panicle but significantly increased grain length. In addition, the GS3 gene-edited plants showed improved taste value, appearance, texture properties, and Rapid Visco Analyser (RVA) profiles. To combine the advantages of both gs3 and dep1, we conducted a molecular design breeding at the GS3 locus of a “super rice” variety, SN265, which has a truncated dep1 allele with erect panicle architecture, high-yield performance, and which is of mediocre eating quality. The elongated grain size of the sn265/gs3 gene-edited plants further increased the grain yield. More importantly, the texture properties and RVA profiles were significantly improved, and the taste quality was enhanced. Beyond showcasing the combined function of dep1 and gs3, this paper presents a strategy for the simultaneous improvement of rice grain yield and quality through manipulating two type C G protein gamma subunits in rice.