Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed

Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa)

Hemp (Cannabis sativa L.) is a versatile crop with substantial potential for creating productive, sustainable, and resilient agricultural systems. However, in contrast to other crops such as cereals, hemp is highly heterozygous, resulting in both challenges and opportunities for agriculture, breeding, and research. Here, we utilise the heterozygosity of hemp to explore the genetic basis of phenotypic variability in a population generated from a single self-pollinated hemp plant. The S1 population shows extensive variability in plant growth, development, and reproductive patterns. Using reduced representation sequencing, selection of alleles heterozygous in the parent plant, and a model originally developed for genome-wide association studies (GWAS), we were able to identify statistically significant single nucleotide variants (SNVs) and haplotypes associated with phenotypic traits of interest, such as flowering time or biomass yield. This new approach, which we term genome-specific association study (GSAS), enables the mapping of traits in a single generation without the need for a large number of diverse cultivars or samples. GSAS might be applicable to other highly heterozygous vegetable and fruit crops, informing the breeding of new cultivars with enhanced uniformity and improved performance in traits relevant to various applications.

Insights into the genetic architecture of the reciprocal interspecific hybrids derived from Chrysanthemum dichrum and C. nankingense

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F1 progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F1 hybrids of diploid C. dichrum (YSJ) and C. nankingense (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting F ST and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01518-0.

Research Progress on the Quality, Extraction Technology, Food Application, and Physiological Function of Rice Bran Oil

Rice bran oil is recommended by the World Health Organization as one of the three major healthy edible oils (along with corn and sesame oils), owing to its unique fatty acid composition and functional components. This study screened, organized, and analyzed a large number of studies retrieved through keyword searches, and investigated the nutritional value and safety of rice bran oil. It reviews the stability of raw rice bran materials and the extraction and refining process of rice bran oil and discusses food applications and sub-health regulations. Research has found that a delayed stabilization treatment of rice bran seriously affects the overall quality of rice bran oil. Compared with traditional solvent extraction, the new extraction technologies have improved the yield and nutritional value of rice bran oil, but most of them are still in the research stage. Owing to the lack of economical and applicable supporting production equipment, extraction is difficult to industrialize, which is a challenging research area for the future. Rice bran oil has stronger antioxidant stability than other edible oils and is more beneficial to human health; however, its application scope and consumption are limited owing to the product price and lack of understanding. Rice bran oil has significant antioxidant, anti-inflammatory, anti-cancer, hypoglycemic, lipid-lowering, and neuroprotective effects. Further exploratory research on other unknown functions is required to lay a scientific basis for the application and development of rice bran oil.

Genome-wide association study and genotypic variation for the major tocopherol content in rice grain

Rice tocopherols, vitamin E compounds with antioxidant activity, play essential roles in human health. Even though the key genes involved in vitamin E biosynthetic pathways have been identified in plants, the genetic architecture of vitamin E content in rice grain remains unclear. A genome-wide association study (GWAS) on 179 genotypically diverse rice accessions with 34,323 SNP markers was conducted to detect QTLs that define total and α- tocopherol contents in rice grains. Total and α-tocopherol contents had a strong positive correlation and varied greatly across the accessions, ranging from 0.230-31.76 and 0.011-30.83 (μg/g), respectively. A total of 13 QTLs were identified, which were spread across five of the rice chromosomes. Among the 13 QTLs, 11 were considered major with phenotypic variation explained (PVE) greater than 10%. Twelve transcription factor (TF) genes, one microprotein (miP), and a transposon were found to be associated with the QTLs with putative roles in controlling tocopherol contents. Moreover, intracellular transport proteins, ABC transporters, nonaspanins, and SNARE, were identified as associated genes on chromosomes 1 and 8. In the vicinity of seven QTLs, protein kinases were identified as key signaling factors. Haplotype analysis revealed the QTLs qAlph1.1, qTot1.1, qAlph2.1, qAlph6.1, qTot6.1, and qTot8.3 to have significant haplogroups. Quantitative RT-PCR validated the expression direction and magnitude of WRKY39 (Os02g0265200), PIP5Ks (Os08g0450800), and MADS59 (Os06g0347700) in defining the major tocopherol contents. This study provides insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in rice and other cereals.

Genome-wide association study and molecular marker development for susceptibility to Gibberella ear rot in maize

KEY MESSAGES

Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed. Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.

Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds

Isoflavone is a secondary metabolite of the soybean phenylpropyl biosynthesis pathway with physiological activity and is beneficial to human health. In this study, the isoflavone content of 205 soybean germplasm resources from 3 locations in 2020 showed wide phenotypic variation. A joint genome-wide association study (GWAS) and weighted gene coexpression network analysis (WGCNA) identified 33 single-nucleotide polymorphisms and 11 key genes associated with soybean isoflavone content. Gene ontology enrichment analysis, gene coexpression, and haplotype analysis revealed natural variations in the Glyma.12G109800 (GmOMT7) gene and promoter region, with Hap1 being the elite haplotype. Transient overexpression and knockout of GmOMT7 increased and decreased the isoflavone content, respectively, in hairy roots. The combination of GWAS and WGCNA effectively revealed the genetic basis of soybean isoflavone and identified potential genes affecting isoflavone synthesis and accumulation in soybean, providing a valuable basis for the functional study of soybean isoflavone.

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.

Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax

Introduction

Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola.

Methods

In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance.

Results

We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs.

Discussion

Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.

Genome-Wide Association Studies of Seven Root Traits in Soybean (Glycine max L.) Landraces

Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits.