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. 2020 Jun;70(3):283-291.
doi: 10.1270/jsbbs.19099. Epub 2020 May 19.

QTL analysis and GWAS of agronomic traits in sweetpotato (Ipomoea batatas L.) using genome wide SNPs

Emdadul Haque  1 , Hiroaki Tabuchi  1 , Yuki Monden  2 , Keisuke Suematsu  1 , Kenta Shirasawa  3 , Sachiko Isobe  3 , Masaru Tanaka  1
Affiliations

QTL analysis and GWAS of agronomic traits in sweetpotato (Ipomoea batatas L.) using genome wide SNPs

Emdadul Haque et al. Breed Sci. 2020 Jun.

Abstract

While sweetpotato (Ipomoea batatas L.) improvement has generally been done by field-based selection, molecular genetic studies on traits of interest, i.e., molecular markers are needed for enhancing the breeding program of this world's 7th most important crop, as such markers facilitate marker-assisted selection. Here, we performed a combined approach of QTLs analyses and GWAS of storage root β-carotene content (BC), dry-matter (DM) and starch content (SC) using the genetic linkage maps constructed with 5,952 and 5,640 SNPs obtained from F1 progenies between cultivars 'J-Red' and 'Choshu'. BC was negatively correlated with DM (r = -0.45) and SC (r = -0.51), while DM was positively correlated with SC (r = 0.94). In both parental maps, a total of five, two and five QTL regions on linkage groups 7 and 8 were associated with BC, DM and SC, respectively. In GWAS of BC, one strong signal (P = 1.04 × 10-9) was observed on linkage group 8, which co-located with one of the above QTL regions. The SNPs markers found here, particularly for β-carotene, would be useful base resources for future marker-assisted selection program with this trait.

Keywords: GWAS; QTL; ddRAD SNPs; root dry-matter; starch; sweetpotato; β-carotene.

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Figures

Fig. 1.
Fig. 1.
Histogram of β-carotene (BC), root dry-matter (DM) and starch content (SC) in the J-Red (J) × Choshu (C) progenies (JCF1). (A) Histogram of BC (absorbance at 455 nm; A455) in 52 JCF1 and their parents. (B) Histogram of DM (%). (C) Histogram of SC (%). Arrows indicate positions of parental cultivars.
Fig. 2.
Fig. 2.
QTLs on linkage maps and associated SNPs for the J parental map. (A) Significant QTLs for BC, DM and SC, which were listed in Supplemental Table 2, are shown in boxes. The selected SNP markers were listed in Table 2, are shown in triangle. QTLs with positive effect are indicated by “+” sign, and those with negative effects were indicated by “–” sign. Position of each QTLs were shown in parenthesis. (B) Manhattan plots from GWAS. Redline is significance threshold of 5% Bonferroni correction. QTLs related to BC, DM and SC are indicated. –log10(P) for each QTLs are shown in parenthesis.
Fig. 3.
Fig. 3.
QTLs on linkage maps and associated SNPs for the C parental map. (A) Significant QTLs for BC, DM and SC, which were listed in Supplemental Table 2, are shown in boxes. The selected SNP markers were listed in Table 2, are shown in triangle. QTLs with positive effect are indicated by “+” sign, and those with negative effects were indicated by “–” sign. Position of each QTLs were shown in parenthesis. (B) Manhattan plots from GWAS. Redline is significance threshold of 5% Bonferroni correction. QTLs related to BC, DM and SC are indicated. –log10(P) for each QTLs are shown in parenthesis.
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