Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.

在自然条件下，通过设计不同的出苗阻力（覆土深度2 cm、4 cm和6 cm）来测定中胚轴伸长潜力不同的水稻种质的出苗速度、成苗率和芽鞘节及中胚轴的长度，以分析影响水稻种子顶土出苗的动力源。结果表明，水稻种子的出苗动力主要来源于芽鞘节间和中胚轴的伸长。在不同阻力处理条件下，不同种质出苗动力差异较大，其中覆土2 cm的不同种质出苗率相差不明显，与室内发芽率结果比较接近，覆土4 cm和覆土6 cm的两个处理不同种质间出苗率差异明显，长胚轴种质出苗速度快，出苗率高，出苗率与室内发芽率相差不大；而短胚轴种质出苗速度慢，出苗率低，其中春江683的出苗率与室内发芽率相比分别下降了6.5和86.2个百分点。研究表明水稻中胚轴的伸长对覆土较深的种子顶土出苗起到关键作用，长胚轴种质顶土出苗动力来自于芽鞘节与中胚轴的共同作用，出苗动力强；而短胚轴顶土出苗动力主要来源于芽鞘节的伸长，出苗动力较弱。还对通过选育长胚轴直播稻品种解决直播稻易倒伏和出苗差等难题的可能性进行了探讨。

中胚轴长度(mesocotyl length, ML)是影响旱直播水稻出苗和早期幼苗活力的重要性状。发掘中胚轴伸长相关位点, 解析其遗传机制, 选育长中胚轴品种是促进旱直播技术推广最为经济和有效的方式。本研究以长中胚轴品种‘Changai’和短中胚轴品种‘IR 145’为亲本构建的F₂遗传分离群体为材料, 构建长池和短池并开展深度重测序(50×)。利用Δ(SNP-index)和G-value两种方法在3号染色体29.56~33.28 Mb处鉴定到1个中胚轴伸长相关位点qML3。在候选区域开发KASP标记, 对184个F₂株系开展连锁分析, 将候选区间缩小到28.89~31.03 Mb。结合基因注释、连锁分析和基因表达分析结果, 推测LOC_Os03g52450、LOC_Os03g56060、LOC_Os03g58290、LOC_Os03g58300、LOC_Os03g58320、LOC_Os03g56050和LOC_Os03g57640为候选基因。这些基因分别与植物激素的调控和细胞分裂相关机制有关。本研究发掘了一个水稻中胚轴伸长相关位点, 对选育长中胚轴品种有一定帮助。

Fast and stable 2-fold accumulation of cytokinins (CKs) was detected initially in roots and then in shoots of 4-day-old wheat (Triticum aestivum L.) seedlings in the course of their treatment with 0.4μM 24-epibrassinolide (EBR). Elevated cytokinin level has been maintained only in the presence of EBR, while the hormone removal has led to return of cytokinin concentration to the control level initially in the roots and then in the shoots. EBR-induced accumulation of cytokinins was accompanied by inhibition of both cytokinin oxidase (CKX) (cytokinin oxidase/dehydrogenase, EC 1.5.99.12) activity and expression of the gene coding for this enzyme, and on the contrary the decline in CKs level resulted in increase in these characteristics up to the control level in roots and then in shoots. Sharp accumulation of cytokinin O-glucosides has been discovered in response to EBR-treatment suggesting fast EBR-induced activation of production of cytokinins, which excessive amounts were transferred into the storage forms. The obtained data provide evidence for the involvement of EBR in regulation of cytokinin level in wheat seedlings.Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Mesocotyl is the crucial organ for pushing buds out of deep water or soil after germination in monocots. Deep direct seeding or mechanized dry seeding cultivation practice requires rice cultivars having long mesocotyl. However, the mechanisms of mesocotyl elongation and domestication remain unknown. Here, our genome-wide association study (GWAS) reveals that natural variations of OsGSK2, a conserved GSK3-like kinase involved in brassinosteroid signaling, determine rice mesocotyl length variation. Variations in the coding region of OsGSK2 alter its kinase activity. It is selected for mesocotyl length variation during domestication. Molecular analyses show that brassinosteroid-promoted mesocotyl elongation functions by suppressing the phosphorylation of an U-type cyclin, CYC U2, by OsGSK2. Importantly, the F-box protein D3, a major positive component in strigolactone signaling, can degrade the OsGSK2-phosphorylated CYC U2 to inhibit mesocotyl elongation. Together, these results suggest that OsGSK2 is selected to regulate mesocotyl length by coordinating strigolactone and brassinosteroid signaling during domestication.

<p class="MsoNormal"> <p class="15"> Rice direct seeding has the significant potential to save labor and water, conserve environmental resources, and reduce greenhouse gas emissions tremendously. &nbsp;Therefore, rice direct seeding is becoming the major cultivation technology applied to rice production in many countries. &nbsp;Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice (DSR) production. &nbsp;This study used a permanent mapping population with 144 recombinant inbred lines (RILs) and 2&nbsp;828 bin-markers to detect quantitative trait loci (QTLs) associated with mesocotyl length in 2019 and 2020. &nbsp;The mesocotyl lengths of the rice RILs and their parents, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), were measured in a growth chamber at 30°C in a dark environment. &nbsp;A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2), 2(4), 3(2), 4, 5, 6, 7, 9, 11(2), and 12. &nbsp;Seven of these QTLs, including <i>qML1a</i>, <i>qML1b</i>, <i>qML2d</i>, <i>qML3a</i>, <i>qML3b</i>, <i>qML5</i>, and <i>qML11b</i>, were reproducibly detected in both years <i>via</i>&nbsp;the interval mapping method. &nbsp;The major QTL, <i>qML3a</i>, was reidentified in two years <i>via</i>&nbsp;the composite interval mapping method. &nbsp;A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb, respectively. &nbsp;Thirteen predicted genes within a relatively small genetic interval (88.18 kb) of the major mesocotyl elongation QTL, <i>qML3a</i>, were more thoroughly analyzed. &nbsp;Finally, the coding DNA sequence variations among SN265, LTH, and Nipponbare indicated that the <i>LOC_Os03g50550</i>&nbsp;gene was the strongest candidate gene for the <i>qML3a</i>&nbsp;QTL controlling the mesocotyl elongation. &nbsp;This <i>LOC_Os03g50550</i>&nbsp;gene encodes a mitogen-activated protein kinase. &nbsp;Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the <i>LOC_Os03g50550</i>&nbsp;gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265. &nbsp;In conclusion, these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation. &nbsp;This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development. </p></p>

Dry direct-seeding of rice is rapidly increasing in China, but variable planting depth associated with machine sowing can lead to low seedling emergence rates. Phenotype analysis of 621 rice accessions showed that mesocotyl length (ML) was induced by deep soil covering and was important in deep-sowing tolerance in the field. Here, we performed and compared GWAS using three types of SNPs (non-synonymous SNP, non-synonymous SNPs and SNPs within promoters and 3 million randomly selected SNPs from the entire set of SNPs) and found that Non-Syn GWAS (GWAS using non-synonyomous SNP) decreased computation time and eliminated confounding by other loci relative to GWAS using randomly selected SNPs. Thirteen QTLs were finally detected, and two new major-effect genes, named OsML1 and OsML2, were identified by an integrated analysis. There were 2 and 7 non-synonymous SNPs in OsML1 and OsML2, respectively, from which 3 and 4 haplotypes were detected in cultivated rice. Combinations of superior haplotypes of OsML1 and OsML2 increased ML by up to 4 cm, representing high emergence rate (85%) in the field with 10 cm of soil cover. The studies provide key loci and naturally occurring alleles ofML that can be used in improving tolerance to dry direct-seeding.

Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (Os01g0269800, Os01g0731100, Os08g0136700, Os08g0137800, and Os08g0137900) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs.

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance.