A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits

Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.

染色体片段代换系（Chromosome segment substitution lines, CSSLs）是定位数量性状基因座（quantitative trait loci, QTL）、分析基因互作，并为图位克隆项目提供起始材料的高效研究工具。本研究报道了在优良水稻品种‘孟加拉’（Bengal）遗传背景下，实现全基因组覆盖的美国杂草稻种质‘PSRR-1’的CSSL文库的构建与表征。多数CSSL仅携带单个明确的杂草稻导入片段，供体基因组的平均导入片段占比为2.8%。本研究将该CSSL群体的多个农艺与驯化性状的QTL定位结果，与两个基于同一杂草稻种质构建的重组自交系（recombinant inbred line, RIL）群体的定位结果进行了对比分析。两类群体中均检测到主效QTL的一致性位点，但CSSL群体中还鉴定到了新的额外QTL。例如，在CSSL群体中于1号、4号和8号染色体上共检测到3个株高主效QTL，其中后两个QTL在两个RIL群体中均未被检出。鉴于多个性状均呈现这一特征，上位性可能是导致杂草稻表型变异的主要成因。杂草稻的高落粒性与种子休眠性，可能由多个微效QTL的累积效应所介导。本研究中鉴定得到的多个携带优良农艺性状（如穗长更长、籽粒更长、千粒重更高）的CSSL，可应用于水稻育种工作。鉴于杂草稻是调控多种杂草相关与农艺性状基因的基因库，该CSSL文库将成为宝贵的研究资源，可用于挖掘潜在遗传多样性以提升作物产量，并通过克隆与表征相关内源基因，解析植物驯化过程。