Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice
Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain...
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| author | Sheikh Maniruzzaman M. Akhlasur Rahman Mehfuz Hasan Mohammad Golam Rasul Abul Hossain Molla Hasina Khatun K. M. Iftekharuddaula Md. Shahjahan Kabir Salma Akter |
| author_facet | Sheikh Maniruzzaman M. Akhlasur Rahman Mehfuz Hasan Mohammad Golam Rasul Abul Hossain Molla Hasina Khatun K. M. Iftekharuddaula Md. Shahjahan Kabir Salma Akter |
| author_sort | Sheikh Maniruzzaman |
| collection | DOAJ |
| description | Achieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F<sub>2:3</sub>) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (<i>boro</i>) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin <i>indica</i> rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied <i>Saltol</i>, <i>SKC1</i>, <i>OsSalT</i>, and sal<i>T</i> locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (<i>qSES1</i>, <i>qSL1</i>, <i>qRL1</i>, <i>qSUR1</i>, <i>qSL8</i>, <i>qK8</i>, <i>qK1</i>) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress. |
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| spelling | doaj.art-7d6f0842cabb497c99f5854e4bc45a332023-11-18T16:48:44ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124131114110.3390/ijms241311141Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in RiceSheikh Maniruzzaman0M. Akhlasur Rahman1Mehfuz Hasan2Mohammad Golam Rasul3Abul Hossain Molla4Hasina Khatun5K. M. Iftekharuddaula6Md. Shahjahan Kabir7Salma Akter8Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshPlant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshDepartment of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, BangladeshDepartment of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, BangladeshDepartment of Environmental Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, BangladeshPlant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshPlant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshPlant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshPlant Physiology Division, Bangladesh Rice Research Institute (BRRI), Gazipur 1701, BangladeshAchieving high-yield potential is always the ultimate objective of any breeding program. However, various abiotic stresses such as salinity, drought, cold, flood, and heat hampered rice productivity tremendously. Salinity is one of the most important abiotic stresses that adversely affect rice grain yield. The present investigation was undertaken to dissect new genetic loci, which are responsible for salt tolerance at the early seedling stage in rice. A bi-parental mapping population (F<sub>2:3</sub>) was developed from the cross between BRRI dhan28/Akundi, where BRRI dhan28 (BR28) is a salt-sensitive irrigated (<i>boro</i>) rice mega variety and Akundi is a highly salinity-tolerant Bangladeshi origin <i>indica</i> rice landrace that is utilized as a donor parent. We report reliable and stable QTLs for salt tolerance from a common donor (Akundi) irrespective of two different genetic backgrounds (BRRI dhan49/Akundi and BRRI dhan28/Akundi). A robust 1k-Rice Custom Amplicon (1k-RiCA) SNP marker genotyping platform was used for genome-wide analysis of this bi-parental population. After eliminating markers with high segregation distortion, 886 polymorphic SNPs built a genetic linkage map covering 1526.5 cM of whole rice genome with an average SNP density of 1.72 cM for the 12 genetic linkage groups. A total of 12 QTLs for nine different salt tolerance-related traits were identified using QGene and inclusive composite interval mapping of additive and dominant QTL (ICIM-ADD) under salt stress on seven different chromosomes. All of these 12 new QTLs were found to be unique, as no other map from the previous study has reported these QTLs in the similar chromosomal location and found them different from extensively studied <i>Saltol</i>, <i>SKC1</i>, <i>OsSalT</i>, and sal<i>T</i> locus. Twenty-eight significant digenic/epistatic interactions were identified between chromosomal regions linked to or unlinked to QTLs. Akundi acts like a new alternate donor source of salt tolerance except for other usually known donors such as Nona Bokra, Pokkali, Capsule, and Hasawi used in salt tolerance genetic analysis and breeding programs worldwide, including Bangladesh. Integration of the seven novel, reliable, stable, and background independent salinity-resilient QTLs (<i>qSES1</i>, <i>qSL1</i>, <i>qRL1</i>, <i>qSUR1</i>, <i>qSL8</i>, <i>qK8</i>, <i>qK1</i>) reported in this investigation will expedite the cultivar development that is highly tolerant to salt stress.https://www.mdpi.com/1422-0067/24/13/11141genetic locisalinity-resilient QTLs (SRQ)salt-tolerant indica germplasm (Akundi)single nucleotide polymorphisms (SNP)1k-RiCA<i>Oryza sativa</i> L. |
| spellingShingle | Sheikh Maniruzzaman M. Akhlasur Rahman Mehfuz Hasan Mohammad Golam Rasul Abul Hossain Molla Hasina Khatun K. M. Iftekharuddaula Md. Shahjahan Kabir Salma Akter Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice International Journal of Molecular Sciences genetic loci salinity-resilient QTLs (SRQ) salt-tolerant indica germplasm (Akundi) single nucleotide polymorphisms (SNP) 1k-RiCA <i>Oryza sativa</i> L. |
| title | Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice |
| title_full | Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice |
| title_fullStr | Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice |
| title_full_unstemmed | Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice |
| title_short | Molecular Mapping to Discover Reliable Salinity-Resilient QTLs from the Novel Landrace Akundi in Two Bi-Parental Populations Using SNP-Based Genome-Wide Analysis in Rice |
| title_sort | molecular mapping to discover reliable salinity resilient qtls from the novel landrace akundi in two bi parental populations using snp based genome wide analysis in rice |
| topic | genetic loci salinity-resilient QTLs (SRQ) salt-tolerant indica germplasm (Akundi) single nucleotide polymorphisms (SNP) 1k-RiCA <i>Oryza sativa</i> L. |
| url | https://www.mdpi.com/1422-0067/24/13/11141 |
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