Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice R&D Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, 210014, China.
Jiangsu Collaborative Innovation Center for Modern Crop Production, 210095, Nanjing, China.
BMC Genomics. 2021 Aug 5;22(1):596. doi: 10.1186/s12864-021-07913-7.
The 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.
Quantitative 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.
By 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.
稻米的食味和蒸煮品质（ECQs）是影响品种推广和市场价值的关键特性。快速粘度分析仪（RVA）测试的淀粉粘度图谱提供了 ECQs 的直接测量方法，代表了与淀粉糊化相关的粘度变化。稻米的 RVA 图谱受复杂的遗传系统控制，也受环境影响。虽然蜡质（Wx）是控制直链淀粉含量（AC）和 ECQs 的主要基因，但仍有其他未知的遗传因素影响 ECQs。
使用来自两个品种 9311 和 Nipponbare 的染色体片段代换系（CSSLs）分析了稻米淀粉糊粘度的数量性状位点（QTLs），这两个品种具有相同的 Wx-b 等位基因。因此，消除了主要位点 Wx 的影响，可以识别与 RVA 图谱相关的其他位点。在中国南京的四年内，测试了七个淀粉 RVA 图谱参数的 QTLs。共鉴定出 310 个 QTL（每个性状 1 至 55 个 QTL），其中 136 个 QTL 在一年以上被鉴定出来。其中，6 个 QTL 在四年内稳定检测到，26 个 QTL 在至少三年内检测到，包括 13 个多效性位点，同时控制 2 至 6 个 RVA 特性。这些稳定的 QTL 热点与几个已知的淀粉合成相关基因（SSRGs）共定位。序列比对显示，两个亲本之间的大多数 SSRGs 的核苷酸和氨基酸序列不同。最后，我们在 Wx 本身附近检测到与多个淀粉粘度性状相关的稳定 QTL，这支持了这样一种观点，即在 Wx 附近还有其他 QTL 控制多个淀粉粘度特征值。
通过消除主要位点 Wx 的贡献，鉴定出与稻米 RVA 图谱相关的多个 QTL，其中一些在四年内稳定检测到。稻米淀粉粘度性状遗传基础的复杂性可能是由于其多效性和多个 QTL 热点。使用染色体片段代换策略鉴定了控制淀粉粘度性状的小 QTL。控制 RVA 图谱特征的 QTL 是在一些已知的 SSRG 区域检测到的，可能是由于等位基因多态性。
