A genome-wide analysis of simple sequence repeats in maize and the development of polymorphism markers from next-generation sequence data

Abstract

BackgroundMaize (Zea mays ssp. mays L.), as the most important plant for staple food of several million people, animal feed and bioenergy productions, is widely cultivated around the world. Simple sequence repeats (SSRs) are widely used as molecular markers in maize genetics and breeding, but only two thousands pairs of SSRs have been published currently, which hardly satisfies for the increasing needs of geneticists and breeders. Furthermore, the increasing studies have revealed that SSRs also play a vital role in functional regulation and evolution. It is fortunate that the development of sequencing technology and bio-software provides the basis for characterization and development of SSRs in maize.ResultsIn this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. Meanwhile, 82,694 (46.02%) SSRs with unique flanking sequences were selected, and then applied to analyze the polymorphism of next-generation sequencing data from 345 maize inbred lines and data from maize reference genome B73. There were 58,946 SSRs with length information results in ten or more than ten genomes, accounting for 71.28% of SSRs with unique flanking sequences, while 55,621 SSRs had polymorphism, with an average PIC value of 0.498. 250 pairs of SSR primers in different genomic regions covering all maize chromosomes were randomly chosen for the experimental validation, with an average PIC value of 0.63 in 11 elite maize inbred lines.ConclusionsOur work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads.

Development of genomewide simple sequence repeat fingerprints and highly polymorphic markers in cucumbers based on next‐generation sequence data

“…A/T motifs were also found to be the most abundant mononucleotide motifs in castor beans, rubber, Cocos nucifera and rice, while C/G motifs were found to be most abundant in sorghum, maize and Ganoderma lucidum. AT/TA motifs were also found to be the most abundant dinucleotide motifs in sorghum and maize, and AG/CT motifs were found to be the most abundant in castor beans, barley, rubber, Cocos nucifera, rice, coffee and mushrooms (Kantety et al 2002, Poncet et al 2006, Zhang et al 2007, Feng et al 2009, Yonemaru et al 2009, Qiu et al 2010, Qian et al 2013, Qu and Liu 2013, Xia et al 2014.…”

Identification of microsatellite loci according to BAC sequencing data and their physical mapping to the bread wheat 5B chromosome

“…Так, анализ результатов секвенирования отдельных хромосом или всего генома ряда злаковых и кукурузы (Zhang et al, 2007;Qu, Liu, 2013;Sergeeva et al, 2014) указывает на то, что наибoлее часто встречаются динуклеотидные повторы, затем частота встречаемости убывает при уве-личении длины повторяющегося мотива. Полученные нами результаты по анализу микросателитных локусов, по данным секвенирования выборки из 130 ВАС-клонов, также указывают на более высокую распространенность динуклеотидных последовательностей (253 последова-тельности), по сравнению с три-(156) и тетра-нуклеотид-ными (27) повторяющимися последовательностями ДНК.…”

“…Встречаемость ди-, три-и тетра-пов-торов варьирует также и в зависимости от участка генома. Оценка распределения ди-и тринуклеотидных повторов в транслируемых и нетранслируемых районах генных локусов показала, что встречающиеся в кодирующих районах генов микросателлиты более чем на 87 % состоят из тринуклеотидов, причем это характерно, например, как для риса, так и для кукурузы (Zhang et al, 2007;Qu, Liu, 2013). Это связано с тем, что увеличение копийности в тринуклеотидном повторе не приводит к сдвигу рамки считывания, и в ряде случаев может поддерживаться естественным отбором.…”

“…Межвидовые различия у злаков заключаются в распространенности разных тринуклео-тидных повторов. Так, по данным анализа последова-тельностей ДНК всего генома кукурузы, выявлено, что наиболее распространенный тринуклеотидный повтор имеет структуру (AGC) n , далее следуют повторы (ACG) n , (CCG) n , (ATC) n , (AAG) n c частотой встречаемости от 2,81 до 2,48 % от общего числа ди-и тринуклеотидных повторов (Qu, Liu, 2013). У риса распределение тринук-леотидных повторов по степени встречаемости несколько иное (Zhang et al, 2007).…”

Positional cloning in maize (Zea mays subsp. mays, Poaceae)

“… Settles et al (2014) have conveniently catalogued these indels (see their Table S1) and shown that 22–31% of these indels are also polymorphic with B73 × W22 and Mo17 × W22 populations, respectively. Resequencing of diverse maize inbred lines has produced more than 100,000 potentially polymorphic SSR loci that have been catalogued ( Qu and Liu, 2013 ; Xu et al, 2013 ). These markers were designed to be polymorphic among a broad diversity of maize lines (including tropical inbreds), and thus may not be polymorphic among the much more closely related inbreds commonly used for forward genetics.…”