Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil\'s high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years\' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera \"CON\" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Rice is the leading global staple crop. Low temperatures pose negative impacts on rice\'s optimal growth and development. Rice cultivars acclimating to low temperatures exhibited improved seedling emergence under direct-seeded sowing conditions, yet little is known about the genes that regulate germination at low temperatures (LTG). In this research investigation, we\'ve performed whole genome sequencing for the 273 rice plant materials. Using the best linear unbiased prediction (BLUP) values for each rice material, we identified 7 LTG-related traits and performed the efficient genetic analysis and genome-wide association study (GWAS). As a result of this, 95 quantitative trait loci (QTLs) and 1001 candidate genes associated with LTG in rice were identified. Haplotype analysis and functional annotation of the candidate genes resulted in the identification of three promising candidate genes (LOC_Os08g30520 for regulating LTG4 and LTG5, LOC_Os10g02625 for regulating LTG6, LTg7 and LTG8, and LOC_Os12g31460 for regulating LTG7, LTg8 and LTG9) involving in the regulation of LTG in rice. This research provides a solid foundation for addressing the LTG issue in rice and will be valuable in future direct-seeded rice breeding programs.

UNASSIGNED: Breeding rice with drought tolerance for harsh environments is crucial for agricultural sustainability. Understanding the genetic underpinnings of drought tolerance is vital for developing resilient rice varieties. Genome-wide association studies (GWAS) have emerged as pivotal tools in unravelling the complex genetic architecture of traits like drought tolerance, capitalizing on the natural genetic diversity within rice germplasm collections.
UNASSIGNED: In this study, a comprehensive panel of 210 rice varieties was phenotyped over ten days in controlled conditions, subjected to simulated drought stress using 20% PEG 6000 in petri dishes. Throughout the stress period, crucial traits such as germination percentage (GP), germination rate index (GRI), mean germination time (MGT), and seedling percentage (SP) were meticulously monitored.
UNASSIGNED: The GWAS analysis uncovered a total of 38 QTLs associated with drought tolerance traits, including novel loci like qMGT-5.2, qSP-3, qSP7.2, and qGP-5.2. Additionally, RNA-seq analysis identified ten genes with significant expression differences under drought stress conditions. Notably, haplotype analysis pinpointed elite haplotypes in specific genes linked to heightened drought tolerance.
UNASSIGNED: Overall, this study underscores the importance of GWAS in validating known genes while unearthing novel loci to enrich the genetic resources for enhancing drought tolerance in rice breeding programs.

Maize (Zea mays L.), a staple food and significant economic crop, is enriched with riboflavin, micronutrients and other compounds that are beneficial for human health. As emphasis on the nutritional quality of crops increases maize research has expanded to focus on both yield and quality. This study exploreed the genetic factors influencing micronutrient levels in maize kernels through a comprehensive genome-wide association study (GWAS). We utilized a diverse panel of 244 inbred maize lines and approximately 3 million single nucleotide polymorphisms (SNPs) to investigate the accumulation of essential and trace elements including cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), selenium (Se) and zinc (Zn). Our analysis identified 842 quantitative trait loci (QTLs), with 12 QTLs shared across multiple elements and pinpointed 524 potential genes within a 100 kb radius of these QTLs. Notably ZmHMA3 has emerged as a key candidate gene previously reported to influence the Cd accumulation. We highlighted ten pivotal genes associated with trace element transport including those encoding heavy metal ATPases, MYB transcription factors, ABC transporters and other crucial proteins involved in metal handling. Additionally, haplotype analysis revealed that eight inbred linesaccumulated relatively high levels of beneficial elements while harmful elements were minimized. These findings elucidate the genetic mechanisms underlying trace element accumulation in maize kernels and provide a foundation for the breeding of nutritionally enhanced maize varieties.

Grain shape is one of the most important factors that affects rice yield. Cloning novel grain shape genes and analyzing their genetic mechanisms are crucial for high yield breeding. In this study, a slender grain CSSL-Z485 with 3-segments substitution in the genetic background of Nipponbare was constructed in rice. Cytological analysis showed that the longer grain length of Z485 was related to the increase in glume cell numbers, while the narrower grain width was associated with the decrease in cell width. Three grain shape-related quantitative trait locus (QTLs), including qGL12, qGW12, and qRLW12, were identified through the F2 population constructed from a cross between Nipponbare and Z485. Furthermore, four single segment substitution lines (SSSLs, S1-S4) carrying the target QTLs were dissected from Z485 by MAS. Finally, three candidate genes of qGL12 for grain length and qGW12 for grain width located in S3 were confirmed by DNA sequencing, RT-qPCR, and protein structure prediction. Specifically, candidate gene 1 encodes a ubiquitin family protein, while candidate genes 2 and 3 encode zinc finger proteins. The results provide valuable germplasm resources for cloning novel grain shape genes and molecular breeding by design.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s11032-024-01480-x.

BACKGROUND: Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits.
RESULTS: QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified.
CONCLUSIONS: These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.

Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.

The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F2 and F2:3 populations derived from the high-yielding hybrid rice variety Chaoyou 1000. We screened 123 pairs of molecular markers, which were available, to construct the genetic linkage map. Subsequently, we assessed the panicle morphology traits of F2 populations in Lingshui County, Hainan Province, in 2017, and F2:3 populations in Hangzhou City, Zhejiang Province, in 2018. These two locations represent two types of ecology. Hangzhou\'s climate is characterized by high temperatures and humidity, while Lingshui\'s climate is characterized by a tropical monsoon climate. In total, 33 QTLs were identified, with eight of these being newly discovered, and two of them were consistently detected in two distinct environments. We identified fourteen QTL-by-environment interactions (QEs), which collectively explained 4.93% to 59.95% of the phenotypic variation. While most of the detected QTLs are consistent with the results of previous tests, the novel-detected QTLs will lay the foundation for rice yield increase and molecular breeding.

Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.

Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.