title: Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.).
abstract: A novel QTL cluster for appearance quality on Chr07 was identified using reciprocal introgression populations in different locations in China. Two secondary F2populations validated QTL with significant effect on appearance quality. Appearance quality (AQ) is the main determinants of market value of rice. Identification of QTL affecting AQ is the prerequisite for efficient improvement of AQ through marker-assisted selection (MAS). Two sets of reciprocal introgression lines derived from indica Minghui 63 and japonica 02428 were used to dissect the stability of QTL affecting five AQ traits, including grain length, grain width, length to width ratio, percentage of grains with chalkiness, and degree of endosperm chalkiness using 4568 bin genotype produced from 58,000 SNPs across five different environments. A total of 41 and 30 main-effect QTL were identified in MH63 and 02428 backgrounds, respectively. Among them, 9 background-independent QTL (BI-QTL) were found. There were also 13 and 10 stable-expressed QTL (SE-QTL) across at least two environments in MH63 and 02428 backgrounds, respectively. Two important BI- and SE-QTL regions (BISERs) including BISER-I harboring qPGWC5, qDEC5, qGW5.1, and qLWR5 on chromosome 5 and BISER-II harboring qGL7, qLWR7, qPGWC7, and qDEC7 on chromosome 7 were identified. The BISER-II was newly reported and validated by two secondary F2populations in the reciprocal backgrounds. Among 59 epistatic QTL (E-QTL) detected in this study, there were only four SE- but no BI-E-QTL detected in different environments, indicating that genetic background has stronger effect on AQ traits than the environmental factors, especially for percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) with lower heritability. BISER-I and BISER-II harboring many BI- and SE-QTL with favorable alleles from slender grain rice are much important for improvement of rice AQ by MAS.
authors.affiliation: Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China.
authors.forename: Xianjin
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.|Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Chen
authors.affiliation: Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China.
authors.forename: Wenkai
authors.initials: W
authors.lastname: Lv
authors.affiliation: Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China.
authors.forename: Xiaoxue
authors.initials: X
authors.lastname: Ou
authors.affiliation: Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.|Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China.
authors.forename: Danying
authors.initials: D
authors.lastname: Xing
authors.affiliation: Hubei Collaborative Innovation Center for Grain Industry / College of Agriculture, Yangtze University, Jingzhou, 434025, China.
authors.forename: Longwei
authors.initials: L
authors.lastname: Yang
authors.affiliation: Institute of Food Crops, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
authors.forename: Fangjun
authors.initials: F
authors.lastname: Fan
authors.affiliation: Institute of Food Crops, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.affiliation: Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. xujlcaas@126.com.|Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. xujlcaas@126.com.|Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. xujlcaas@126.com.
authors.forename: Jianlong
authors.initials: J
authors.lastname: Xu
authors.affiliation: Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. tonyztq@163.com.
authors.forename: Tianqing
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.|Shenzhen Institute of Breeding for Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D002523:Edible Grain / Q000235:genetics; D004777:Environment; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics*