맥주보리의 large-InDel 마커 개발을 위한 whole genome re-sequencing의 이용
Utilization of whole genome re-sequencing for large-InDel Markers Development in Malting Barley
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초록
Barley is an economically important cereal crop grown under diverse environmental conditions and ranked fourth in terms of productionvolume. Barley is a diploid self-fertilizing plant with seven chromosomes, and has a 5.1 Gbp genome with more than 80% repeat sequences. Whole genome re-sequencing (WGR) has provided substantial information on sequence variation distributed on all chromosomes, such as singlenucleotide polymorphisms, insertions, and deletions, which are used in the development of DNA markers. In this study, we performed WGRto detect sequence variations among six Korean malting varieties. An average of 92,552 insertions and deletions (InDels) were detected inthese varieties in comparison to the high-quality reference genome sequences. The InDel density of the six Korean malting varieties rangedfrom 17 to 19 InDel/1Mbp with an average of 18 InDel/1Mbp. No InDel could be detected in 193 regions in all chromosomes except chr. unassigned. One interval with high-density InDel, more than 150 InDel/1Mbp, was located on the 1H, 3H, 6H, and 7H chromosomes. Atotal of 145 InDel markers were developed using 225 large-InDel markers, longer than 50 bp. Seventeen large-InDel makers showedpolymorphisms among 31 malting barley varieties. These 31 malting barley varieties were divided into four groups based on phylogeneticanalysis. These results presented a development method of agarose-resolvable large-InDel markers using WGR. Seventeen polymorphic large-InDelmarkers were used to conserve and identify barley germplasms. This vast information on sequence variation in six Korean malting barleyscould be used for the development of DNA markers and marker-assisted selection.
Abstract
Barley is an economically important cereal crop grown under diverse environmental conditions and ranked fourth in terms of productionvolume. Barley is a diploid self-fertilizing plant with seven chromosomes, and has a 5.1 Gbp genome with more than 80% repeat sequences. Whole genome re-sequencing (WGR) has provided substantial information on sequence variation distributed on all chromosomes, such as singlenucleotide polymorphisms, insertions, and deletions, which are used in the development of DNA markers. In this study, we performed WGRto detect sequence variations among six Korean malting varieties. An average of 92,552 insertions and deletions (InDels) were detected inthese varieties in comparison to the high-quality reference genome sequences. The InDel density of the six Korean malting varieties rangedfrom 17 to 19 InDel/1Mbp with an average of 18 InDel/1Mbp. No InDel could be detected in 193 regions in all chromosomes except chr. unassigned. One interval with high-density InDel, more than 150 InDel/1Mbp, was located on the 1H, 3H, 6H, and 7H chromosomes. Atotal of 145 InDel markers were developed using 225 large-InDel markers, longer than 50 bp. Seventeen large-InDel makers showedpolymorphisms among 31 malting barley varieties. These 31 malting barley varieties were divided into four groups based on phylogeneticanalysis. These results presented a development method of agarose-resolvable large-InDel markers using WGR. Seventeen polymorphic large-InDelmarkers were used to conserve and identify barley germplasms. This vast information on sequence variation in six Korean malting barleyscould be used for the development of DNA markers and marker-assisted selection.
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