Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content

Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.

Amino acid transporter gene TaATLa1 from Triticum aestivum L. improves growth under nitrogen sufficiency and is down regulated under nitrogen deficiency

TaATLa1 was identified to respond to nitrogen deprivation through transcriptome analysis of wheat seedlings. TaATLa1 specifically transports Gln, Glu, and Asp, and affects the biomass of Arabidopsis and wheat. Nitrogen is an essential macronutrient and plays a crucial role in wheat production. Amino acids, the major form of organic nitrogen, are remobilized by amino acid transporters (AATs) in plants. AATs are commonly described as central components of essential developmental processes and yield formation via taking up and transporting amino acids in plants. However, few studies have reported the detailed biochemical properties and biological functions of these AATs in wheat. In this study, key genes encoding AATs were screened from transcriptome analysis of wheat seedlings treated with normal nitrogen (NN) and nitrogen deprivation (ND). Among them, 21 AATs were down-regulated and eight AATs were up-regulated under ND treatment. Among the homoeologs, TaATLa1.1-3A, TaATLa1.1-3B, and TaATLa1.1-3D (TaATLa1.1-3A, -3B, and -3D), belonging to amino acid transporter-like a (ATLa) subfamily, were significantly down-regulated in response to ND in wheat, and accordingly were selected for functional analyses. The results demonstrated that TaATLa1.1-3A, -3B, and -3D effectively transported glutamine (Gln), glutamate (Glu), and aspartate (Asp) in yeast. Overexpression of TaAILa1.1-3A, -3B, and -3D in Arabidopsis thaliana L. significantly increased amino acid content in leaves, storage protein content in seeds and the plant biomass under NN. Knockdown of TaATLa1.1-3A, -3B, and -3D in wheat seedlings resulted in a significant block of amino acid remobilization and growth inhibition. Taken together, TaATLa1.1-3A, -3B, and -3D contribute substantially to Arabidopsis and wheat growth. We propose that TaATLa1.1-3A, -3B, and -3D may participate in the source-sink translocation of amino acid, and they may have profound implications for wheat yield improvement.

Genetic mapping high protein content QTL from soybean 'Nanxiadou 25' and candidate gene analysis

BACKGROUND

Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean.

RESULTS

In this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20-1 and qSPC_20-2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20-1 and qSPC_20-2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait.

CONCLUSIONS

These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.

Transcriptome analysis reveals the mechanism by which spraying diethyl aminoethyl hexanoate after anthesis regulates wheat grain filling

BACKGROUND

Diethyl aminoethyl hexanoate (DA-6), a plant growth regulator, has many beneficial effects on agricultural production. DA-6 has been applied to many plant species, but the molecular mechanism by which spraying DA-6 after anthesis regulates wheat grain filling is still unknown.

RESULTS

In this study, we used four DA-6 concentrations: C0 (0 g/L), C2 (2 g/L), C4 (4 g/L), and C6 (6 g/L). The results showed that C4 and C6 led to a significantly higher 1000-grain weight and seed protein content than C0 during two wheat growing seasons. We then subjected samples at 24 days after anthesis (at which point the grain weight increased rapidly) to transcriptome analysis. Flag leaf (L), seed (S), and stem (T) samples under C6 and C0 were used for RNA-seq. The seed samples under C6 compared with C0 (S6vsS0) presented the most differentially expressed genes (DEGs; 2164). Plant hormone signal transduction (p = 1.97 × 10^- 4), protein processing in the endoplasmic reticulum (ER; p = 9.04 × 10^- 11) and starch and sucrose metabolism (p = 1.90 × 10^- 10) pathways were the most markedly enriched pathways in the flag leaves, stems, and seeds, respectively. DEGs involved in sucrose synthesis in the flag leaves, protein processing in ER in the stems, and starch synthesis and protein processing in ER in the seeds were significantly upregulated under C6 compared with C0.

CONCLUSIONS

Overall, we propose a model for spraying DA-6 after anthesis to regulate metabolic pathways in wheat, which provides new insights into wheat in response to DA-6.

A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection

BACKGROUND

Seeds of domesticated barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of barley.

RESULTS

To uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17 kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis.

CONCLUSION

Our findings provide evidence of the pervasiveness of the 17 kb deletion in spring barley from different geographic regions and at the same time reveal genomic footprints of selection in naked barley, which follow both geographic and morphological patterns.

Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions

Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0.05 were detected across the 20 chromosomes (Chr), with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein and oil content. Of the 31 SNPs that were associated with the two target traits, 31 beneficial alleles were identified. Two SNP markers, namely rs15774585 and rs15783346 on Chr 07, were determined to be related to seed oil content both in 2015 and 2016. Three SNP markers, rs53140888 on Chr 01, rs19485676 on Chr 13, and rs24787338 on Chr 20 were correlated with seed protein content both in 2015 and 2016. These beneficial alleles may potentially contribute towards the MAS of favorable soybean protein and oil characteristics.

Development of sequence-based markers for seed protein content in pigeonpea

Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F₂ population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

BACKGROUND

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.

RESULTS

The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.

CONCLUSIONS

Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.