Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat (Fagopyrum esculentum).

Yang Liu,Zelin Yi,Xiaomei Fang,Tian Tang,Jinyu Luo,Kaixuan Zhang,Meiliang Zhou,Renwu Ruan,Yingqian Wang,Jian Zhang,Yinhuan Wu,Yudong Wang,Haotian Wu

doi:10.3390/plants11060742

Abstract

Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.

Highlights

IntroductionCommon buckwheat (Fagopyrum esculentum Moench) is a medicinal and edible crop that belongs to the eudicot family Polygonaceae [1]
Introduction published maps and institutional affilCommon buckwheat (Fagopyrum esculentum Moench) is a medicinal and edible crop that belongs to the eudicot family Polygonaceae [1]
The raw reads were uploaded in the NCBI Sequence Read Archive (SRA) under the accession numbers

Summary

Introduction

Common buckwheat (Fagopyrum esculentum Moench) is a medicinal and edible crop that belongs to the eudicot family Polygonaceae [1]. Due to its characteristics of a shorter growing period, wide adaptability to different geographical environments, and strong resistance to extreme climates, common buckwheat is widely cultivated in temperate regions of Asia, Europe, and North America [2]. Common buckwheat seeds are rich in protein, fat, starch, vitamin, rutin, mineral elements, and vegetable cellulose, and it has preventive and therapeutic effects on cardiovascular diseases, diabetes, and constipation [3]. Common buckwheat has high nutritional value, the seed yield is low because of its self-incompatibility. The lack of genomic resources and tightly linked markers of important agronomic genes of buckwheat is an important factor restricting the molecular iations

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