Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum DOI Creative Commons
Nate Korth, Qinnan Yang, Mallory J. Van Haute

et al.

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(9)

Published: July 9, 2024

Substantial functional metabolic diversity exists within species of cultivated grain crops that directly or indirectly provide more than half all calories consumed by humans around the globe. While such is molecular currency used for improving agronomic traits, poorly characterized its effects on human nutrition and utilization gut microbes. Moreover, we know little about traits' potential tradeoffs pleiotropic nutritional traits. Here, applied a quantitative genetics approach using meta-analysis parallel genome-wide association studies Sorghum bicolor traits describing changes in composition function microbe communities, any 200 sorghum seed across diverse population to identify associated genetic variants. A total 15 multiple-effect loci (MEL) were initially found where different alleles genome produced affected abundance multiple bacterial taxa 2 microbiomes automated vitro fermentations. Next, conducted seed, biochemical, same identified significant associations boundaries 13/15 MEL microbiome In several instances, colocalization variation affecting provided hypotheses causal mechanisms through which could affect both This work demonstrates factors can also drive microbes, particularly considered beneficial. Understanding these relationships will inform future strategies crop improvement toward yield, sustainability, health.

Language: Английский

Contents of tannins of cultivars of sorghum cultivated in Brazil, as determined by four quantification methods DOI

C. Palacios,

Alice Nagai, Priscila Bezerra Torres

et al.

Food Chemistry, Journal Year: 2020, Volume and Issue: 337, P. 127970 - 127970

Published: Sept. 3, 2020

Language: Английский

Citations

82
Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity DOI Creative Commons
J. Lucas Boatwright, Sirjan Sapkota, Hongyu Jin

et al.

The Plant Journal, Journal Year: 2022, Volume and Issue: 111(3), P. 888 - 904

Published: June 2, 2022

Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring variation across diverse accessions. We report whole-genome sequencing (WGS) 400 sorghum (Sorghum bicolor (L.) Moench) accessions from Sorghum Panel (SAP) at an average coverage 38× (25-72×), enabling development a high-density genomic marker set 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) 5 copy number (CNVs) 170 000). observe slightly more deletions among indels much higher prevalence CNVs compared insertions. This new enabled identification several novel putative associations height tannin content, which were not identified when using previous lower-density sets. WGS scored in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half all genome falling into this category. The predictive ability best unbiased linear predictor (GBLUP) models was increased 30% markers rather than GBS markers. 18 selection peaks subpopulations that formed due evolutionary divergence during domestication, we found six Fst resulting comparisons between converted lines within SAP distinct associated historic selection. population has served continues as significant public resource research demonstrates value improving upon existing resources.

Language: Английский

Citations

47
GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing DOI Creative Commons
Liyi Zhang, Jianxia Xu, Yanqing Ding

et al.

Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(4)

Published: March 23, 2023

Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors China. Since tannins play an important role liquor brewing, accurately understanding the relationship between can provide basis selection standards sorghum. We resequenced panel 242 accessions performed population structure genome-wide association study (GWAS) identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, content. Phylogenetic analysis, principal component analysis (PCA), admixture model infer structure. Two distinct genetic sub-populations according their corresponding northern southern geographic origin. To investigate natural variation GWAS with 2,760,264 SNPs conducted four environments using multiple models (Blink, FarmCPU, GLM, MLM). be associated exocarp, mesocarp, testa, on all chromosomes except chromosome 5, which 47 might novel QTL. Some found colocalize orthologous genes flavonoid biosynthetic pathway from other plants, including Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 AT5G41220 (GST), as well rice (Oryza sativa) MYB61 OsbHLH025. Our investigation germplasm may help guide future breeding brewing.

Language: Английский

Citations

23
A telomere-to-telomere genome assembly of Hongyingzi, a sorghum cultivar used for Chinese Baijiu production DOI Creative Commons
Yanqing Ding, Yilin Wang, Jianxia Xu

et al.

The Crop Journal, Journal Year: 2024, Volume and Issue: 12(2), P. 635 - 640

Published: March 29, 2024

Sorghum (Sorghum bicolor (L.) Moench) is a world cereal crop used in China for producing Baijiu, distilled spirit. We report telomere-to-telomere genome assembly of the Baijiu cultivar Hongyingzi, HYZ-T2T, using ultralong reads. The 10 chromosome pairs contained 33,462 genes, which 93% were functionally annotated. 20 telomeres and centromeric regions on HYZ-T2T chromosomes predicted two consecutive large inversions 2 characterized. A 65-gene reconstruction metabolic pathway tannins, flavor substances was performed may advance breeding sorghum cultivars production.

Language: Английский

Citations

9
Natural variations in TT8 and its neighboring STK confer yellow seed with elevated oil content in Brassica juncea DOI Creative Commons
Lunwen Qian,

Liu Yang,

Xianjun Liu

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(5)

Published: Jan. 30, 2025

Seed color is a critical quality trait in numerous plant species. In oilseed Brassica crops, including rapeseed and mustard, yellow seeds are distinguished by their significantly higher oil content faster germination rates compared to black or brown counterparts. Despite the agronomic significance of being prime breeding target, mechanisms underlying elevated remain obscure. this study, we assembled first telomere-to-telomere (T2T) genome B. juncea further investigated genetic regulation, molecular mechanism, evolutionary history juncea. Through an analysis allelic variation TRANSPARENT TESTA 8 ( TT8 ) genes across 1,002 worldwide B . accessions, traced single origin approximately 2,300 y ago Southwestern China. Furthermore, discovered MADS-box gene SEEDSTICK STK coevolved with , they coordinately regulated seed size, accumulation, coat proportion These findings open broad avenues for targeted yellow-seeded crops content.

Language: Английский

Citations

1
Qualitative and Quantitative Analysis of Sorghum Grain Composition Including Protein and Tannins Using ATR-FTIR Spectroscopy DOI

Haijing Lin,

Scott R. Bean, Michael Tilley

et al.

Food Analytical Methods, Journal Year: 2020, Volume and Issue: 14(2), P. 268 - 279

Published: Oct. 14, 2020

Language: Английский

Citations

52
Sorghum genetic, genomic, and breeding resources DOI Creative Commons
Zhanguo Xin, Mingli Wang, Hugo E. Cuevas

et al.

Planta, Journal Year: 2021, Volume and Issue: 254(6)

Published: Nov. 5, 2021

Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, breeding resources that are now available researchers plant breeders. As world faces challenges of a rising population changing global climate, new agricultural solutions will need be developed address food fiber needs future. To end, sorghum invaluable crop species as it is stress-resistant C4 well adapted for semi-arid arid regions. already remained staple in many parts Africa Asia critically important animal feed niche culinary applications other regions, such United States. In addition, begun into promising feedstock forage bioenergy production. Due this increasing demand its potential these needs, continuous development powerful community required. These include vast collections germplasm, high-quality reference genome sequences, association panels genome-wide studies traits involved production, mutant populations rapid discovery causative genes phenotypes relevant improvement, gene expression atlas, online databases integrate all provide with tools can used genomic studies. Used tandem, valuable ensure rate, quality, collaborative ongoing improvement efforts able rival major crops.

Language: Английский

Citations

45
Natural variation in Glume Coverage 1 causes naked grains in sorghum DOI Creative Commons
Peng Xie, Sanyuan Tang, Chengxuan Chen

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Feb. 25, 2022

Abstract One of the most critical steps in cereal threshing is ease with which seeds are detached from sticky glumes. Naked grains low glume coverage have dramatically increased efficiency and seed quality. Here, we demonstrate that GC1 ( Glume Coverage 1 ), encoding an atypical G protein γ subunit, negatively regulates sorghum coverage. Naturally truncated variations C-terminus accumulate at higher levels affect stability a patatin-related phospholipase SbpPLAII-1. A strong positive selection signature around genic region found naked cultivars. Our findings reveal crucial event during domestication through subtle regulation development by variation, establish strategy for future breeding grains.

Language: Английский

Citations

31
African cereal fermentations: A review on fermentation processes and microbial composition of non-alcoholic fermented cereal foods and beverages DOI

Felicitas Pswarayi,

Michael G. Gänzle

International Journal of Food Microbiology, Journal Year: 2022, Volume and Issue: 378, P. 109815 - 109815

Published: June 21, 2022

Language: Английский

Citations

30
The quest for the perfect loaf of sourdough bread continues: Novel developments for selection of sourdough starter cultures DOI
Michael G. Gänzle, Nanzhen Qiao, Julia Bechtner

et al.

International Journal of Food Microbiology, Journal Year: 2023, Volume and Issue: 407, P. 110421 - 110421

Published: Oct. 4, 2023

Language: Английский

Citations

20