High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq)
Cotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 a...
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2025-01-01
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| author | Changcai Teng Hongyan Zhang Wanwei Hou Ping Li Xianli Zhou Yujiao Liu |
| author_facet | Changcai Teng Hongyan Zhang Wanwei Hou Ping Li Xianli Zhou Yujiao Liu |
| author_sort | Changcai Teng |
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| description | Cotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 and the green cotyledon variety Qingcan 17 as parent plants to construct hybrid combinations. F<sub>1</sub>-, F<sub>2</sub>-, BC<sub>1</sub>F<sub>1</sub>-, and BC<sub>2</sub>F<sub>1</sub>-generation single-plant cotyledon colors were counted to clarify cotyledon color inheritance. F<sub>2</sub>-generation individuals were genotyped using ddRAD-Seq to construct a genetic linkage map and identify QTLs for cotyledon color. Green cotyledons were controlled by one pair of recessive nuclear genes. Using the screened 1991 SNP markers, a high-density linkage map was constructed, with a coverage length of 1476.95 cM and an average map distance of 0.96 cM. The green cotyledon trait was located using WinQTL Cart, and a <i>vfGC</i> candidate interval explaining 34.30 to 49.40% of the phenotypic variation was identified at LG02 (101.952 cM to 115.493 cM) and at LOD = 16.0, corresponding to chr1L 1,077,051,302 bp to 1,636,400,339 bp (559.35 Mb). The above interval contained 2021 genes, 20 of which were involved in photosynthesis, but no <i>SGR</i> or genes with similar functions were identified. However, the published faba bean <i>vfSGR</i> was located within the <i>vfGC</i> candidate interval, confirming that our localization interval was reliable. The above findings provided further clues for the fine localization of genes regulating green cotyledons and the development of molecular linked markers in faba bean. |
| format | Article |
| id | doaj-art-147534ca327b476ba8ce1b5871b038d1 |
| institution | Kabale University |
| issn | 2073-4395 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Agronomy |
| spelling | doaj-art-147534ca327b476ba8ce1b5871b038d12025-01-24T13:17:07ZengMDPI AGAgronomy2073-43952025-01-0115119310.3390/agronomy15010193High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq)Changcai Teng0Hongyan Zhang1Wanwei Hou2Ping Li3Xianli Zhou4Yujiao Liu5Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, ChinaCotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 and the green cotyledon variety Qingcan 17 as parent plants to construct hybrid combinations. F<sub>1</sub>-, F<sub>2</sub>-, BC<sub>1</sub>F<sub>1</sub>-, and BC<sub>2</sub>F<sub>1</sub>-generation single-plant cotyledon colors were counted to clarify cotyledon color inheritance. F<sub>2</sub>-generation individuals were genotyped using ddRAD-Seq to construct a genetic linkage map and identify QTLs for cotyledon color. Green cotyledons were controlled by one pair of recessive nuclear genes. Using the screened 1991 SNP markers, a high-density linkage map was constructed, with a coverage length of 1476.95 cM and an average map distance of 0.96 cM. The green cotyledon trait was located using WinQTL Cart, and a <i>vfGC</i> candidate interval explaining 34.30 to 49.40% of the phenotypic variation was identified at LG02 (101.952 cM to 115.493 cM) and at LOD = 16.0, corresponding to chr1L 1,077,051,302 bp to 1,636,400,339 bp (559.35 Mb). The above interval contained 2021 genes, 20 of which were involved in photosynthesis, but no <i>SGR</i> or genes with similar functions were identified. However, the published faba bean <i>vfSGR</i> was located within the <i>vfGC</i> candidate interval, confirming that our localization interval was reliable. The above findings provided further clues for the fine localization of genes regulating green cotyledons and the development of molecular linked markers in faba bean.https://www.mdpi.com/2073-4395/15/1/193cotyledon colorddRAD-seqfaba beangenetic map |
| spellingShingle | Changcai Teng Hongyan Zhang Wanwei Hou Ping Li Xianli Zhou Yujiao Liu High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) Agronomy cotyledon color ddRAD-seq faba bean genetic map |
| title | High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) |
| title_full | High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) |
| title_fullStr | High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) |
| title_full_unstemmed | High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) |
| title_short | High-Density Genetic Map Construction and QTL Detection for Cotyledon Color in Faba Bean Based on Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq) |
| title_sort | high density genetic map construction and qtl detection for cotyledon color in faba bean based on double digest restriction site associated dna sequencing ddrad seq |
| topic | cotyledon color ddRAD-seq faba bean genetic map |
| url | https://www.mdpi.com/2073-4395/15/1/193 |
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