Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

نویسندگان

  • Sanzhen Liu
  • Jun Zheng
  • Pierre Migeon
  • Jie Ren
  • Ying Hu
  • Cheng He
  • Hongjun Liu
  • Junjie Fu
  • Frank F. White
  • Christopher Toomajian
  • Guoying Wang
چکیده

The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1.

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to > 75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly r...

متن کامل

Matrix Attachment Regions and Transcribed Sequences within a Long Chromosomal Continuum Containing Maize Adh7

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to >75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly re...

متن کامل

Molecular population genetics of maize regulatory genes during maize evolution By

Maize was domesticated from its wild ancestor, teosinte, in southern Mexico between ~6,250 and ~10,000 years ago. The domestication of maize resulted in an extensive phenotypic change in female inflorescence (ear) structures from teosinte. MADS-box genes encode transcription factors which are key regulators of plant inflorescence and flower development. We examined DNA sequence variation in 32 ...

متن کامل

Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize

Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid clea...

متن کامل

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Following the domestication of maize over the past approximately 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره 7  شماره 

صفحات  -

تاریخ انتشار 2017