Stalk lodging, which is generally determined by stalk strength, results in considerable yield loss and has become a primary threat to maize (Zea mays) yield under high-density planting. However, the molecular genetic basis of maize stalk strength remains unclear, and improvement methods remain inefficient. Here, we combined map-based cloning and association mapping and identified the gene stiff1 underlying a major quantitative trait locus for stalk strength in maize. A 27.2-kb transposable element insertion was present in the promoter of the stiff1 gene, which encodes an F-box domain protein. This transposable element insertion repressed the transcription of stiff1, leading to the increased cellulose and lignin contents in the cell wall and consequently greater stalk strength. Furthermore, a precisely edited allele of stiff1 generated through the CRISPR/Cas9 system resulted in plants with a stronger stalk than the unedited control. Nucleotide diversity analysis revealed that the promoter of stiff1 was under strong selection in the maize stiff-stalk group. Our cloning of stiff1 reveals a case in which a transposable element played an important role in maize improvement. The identification of stiff1 and our edited stiff1 allele pave the way for efficient improvement of maize stalk strength.

• MeSH
• alely MeSH
• buněčná stěna metabolismus   MeSH
• CRISPR-Cas systémy MeSH
• fenotyp MeSH
• kukuřice setá genetika   MeSH
• lignin metabolismus   MeSH
• lokus kvantitativního znaku MeSH
• mapování chromozomů MeSH
• promotorové oblasti (genetika) * MeSH
• rostlinné geny MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• sekvenční analýza MeSH
• transformace genetická MeSH
• transpozibilní elementy DNA genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Kinetoplastid flagellates are known for several unusual features, one of which is their complex mitochondrial genome, known as kinetoplast (k) DNA, composed of mutually catenated maxi- and minicircles. Trypanosoma lewisi is a member of the Stercorarian group of trypanosomes which is, based on human infections and experimental data, now considered a zoonotic pathogen. By assembling a total of 58 minicircle classes, which fall into two distinct categories, we describe a novel type of kDNA organization in T. lewisi. RNA-seq approaches allowed us to map the details of uridine insertion and deletion editing events upon the kDNA transcriptome. Moreover, sequencing of small RNA molecules enabled the identification of 169 unique guide (g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs. The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledge of the structure and expression of the mitochondrial genomes of these human and animal pathogens. Finally, a scenario describing the evolution of minicircles is presented.

• MeSH
• adenosintrifosfatasy genetika   MeSH
• editace RNA MeSH
• fylogeneze MeSH
• genom mitochondriální MeSH
• guide RNA, Kinetoplastida genetika   MeSH
• mitochondrie genetika   MeSH
• podjednotky proteinů genetika   MeSH
• protozoální DNA genetika   MeSH
• RNA protozoální genetika   MeSH
• Trypanosoma lewisi genetika   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Sweet maize and popcorn retain tillering growth habit during maize diversification. However, the underlying molecular genetic mechanism remains unknown. Here, we show that the retention of maize tillering is controlled by a major quantitative trait locus (QTL), tin1, which encodes a C2H2-zinc-finger transcription factor that acts independently of tb1. In sweet maize, a splice-site variant from G/GT to C/GT leads to intron retention, which enhances tin1 transcript levels and consequently increases tiller number. Comparative genomics analysis and DNA diversity analysis reveal that tin1 is under parallel selection across different cereal species. tin1 is involved in multiple pathways, directly represses two tiller-related genes, gt1 and Laba1/An-2, and interacts with three TOPLESS proteins to regulate the outgrowth of tiller buds. Our results support that maize tin1, derived from a standing variation in wild progenitor teosinte population, determines tillering retention during maize diversification.

• MeSH
• fenotyp MeSH
• genetické lokusy MeSH
• kukuřice setá genetika   růst a vývoj   metabolismus   MeSH
• lokus kvantitativního znaku MeSH
• regulace genové exprese u rostlin MeSH
• rostlinné geny genetika   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• vývoj rostlin genetika   fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The applications of semi-dwarf genes such as sd1 and Rht1 in rice and wheat resulted in the first "green revolution" in the 1960s. However, such semi-dwarf genes that can efficiently reduce plant stature and have few negative yield traits have not yet been identified in maize. In this study, a new allele of Brachytic2 gene (qpa1) encoding P-glycoprotein was rapidly fine-mapped using a modified method. The qpa1, containing a 241-bp deletion in the last exon, had no negative effect on yield, but greatly modified the plant architecture including significantly reduced plant height and ear height, increased stalk diameter and erected leaf. A common variant similar to maize qpa1 was also present in the sorghum orthologous dw3 locus. Comparative RNA-seq analysis next showed 99 differentially co-expressed genes affected by Br2 in maize and dw3 in sorghum, including four plant height genes D3, BAK1, Actin7 and Csld1, which are involved in gibberellin and brassinosteroid biosynthesis, auxin transport and cellulose synthesis. The qpa1 can be applied to efficiently modify plant stature in maize and in combination with D3, BAK1, Actin7, Csld1 and the other 95 differentially co-expressed genes, can be edited using new genomic editing tools for further applications and studies.

• MeSH
• alely * MeSH
• chromozomy rostlin MeSH
• fenotyp * MeSH
• genetické asociační studie * MeSH
• genom rostlinný MeSH
• genomika metody   MeSH
• inbreeding MeSH
• kukuřice setá genetika   MeSH
• kvantitativní znak dědičný MeSH
• lokus kvantitativního znaku MeSH
• mapování chromozomů MeSH
• rostlinné geny * MeSH
• sekvenční analýza RNA MeSH
• šlechtění rostlin MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

• MeSH
• DNA rostlinná genetika   MeSH
• genetická variace MeSH
• genetické lokusy MeSH
• jedlá semena genetika   MeSH
• klonování DNA MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• párování bází genetika   MeSH
• rostlinné geny * MeSH
• rostlinné proteiny chemie   genetika   MeSH
• rýže (rod) genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• sekvenční delece MeSH
• sekvenční seřazení MeSH
• selekce (genetika) MeSH
• Setaria (rostlina) genetika   MeSH
• Sorghum genetika   MeSH
• terciární struktura proteinů MeSH
• zemědělství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH