Dataset Information

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.).

ABSTRACT: Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely elusive. In the present study, a linkage analysis for seed dormancy and germination behavior was conducted using a set of 146 chromosome segment substitution lines (CSSLs), of which each carries a single or a few chromosomal segments of Nipponbare (NIP) in the background of Zhenshan 97 (ZS97). A total of 36 quantitative trait loci (QTLs) for six germination parameters were identified. Among them, qDOM3.1 was validated as a major QTL for seed dormancy in a segregation population derived from the qDOM3.1 near-isogenic line, and further delimited into a genomic region of 90 kb on chromosome 3. Based on genetic analysis and gene expression profiles, the candidate genes were restricted to eight genes, of which four were responsive to the addition of abscisic acid (ABA). Among them, LOC_Os03g01540 was involved in the ABA signaling pathway to regulate seed dormancy. The results will facilitate cloning the major QTLs and understanding the genetic architecture for seed dormancy and germination in rice and other crops.

SUBMITTER: Yuan S

PROVIDER: S-EPMC7072991 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (<i>Oryza sativa</i> L.).

Yuan Shaowen S Wang Yuntong Y Zhang Chaopu C He Hanzi H Yu Sibin S

International journal of molecular sciences 20200217 4

Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely elusive. In the present study, a linkage analysis for seed dormancy and germination behavior was conducted using a set of 146 chromosome segment substitution lines (CSSLs), of which each ca ...[more]

PMID: 32079255

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Project description:BackgroundThe eating and cooking qualities (ECQs) of rice (Oryza sativa L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a direct measure of ECQs and represent the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and are also affected by the environment. Although Waxy (Wx) is the major gene controlling amylose content (AC) and ECQs, there are still other unknown genetic factors that affect ECQs.ResultsQuantitative trait loci (QTLs) for starch paste viscosity in rice were analyzed using chromosome segment substitution lines (CSSLs) developed from the two cultivars 9311 and Nipponbare, which have same Wx-b allele. Thus, the effect of the major locus Wx was eliminated and the other locus associated with the RVA profile could be identified. QTLs for seven parameters of the starch RVA profile were tested over four years in Nanjing, China. A total of 310 QTLs were identified (from 1 to 55 QTLs per trait) and 136 QTLs were identified in more than one year. Among them, 6 QTLs were stalely detected in four years and 26 QTLs were detected in at least three years including 13 pleiotropic loci, controlling 2 to 6 RVA properties simultaneously. These stable QTL hotspots were co-located with several known starch synthesis-related genes (SSRGs). Sequence alignments showed that nucleotide and amino acid sequences of most SSRGs were different between the two parents. Finally, we detected stable QTLs associated with multiple starch viscosity traits near Wx itself, supporting the notion that additional QTLs near Wx control multiple characteristic values of starch viscosity.ConclusionsBy eliminating the contribution from the major locus Wx, multiple QTLs associated with the RVA profile of rice were identified, several of which were stably detected over four years. The complexity of the genetic basis of rice starch viscosity traits might be due to their pleiotropic effects and the multiple QTL hot spots. Minor QTLs controlling starch viscosity traits were identified by using the chromosome segment substitution strategy. Allele polymorphism might be the reason that QTLs controlling RVA profile characteristics were detected in some known SSRG regions.

Dataset Information

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.).

Publications

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (<i>Oryza sativa</i> L.).

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