Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

Abstract

Background: The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice. Results: We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis. Conclusions: In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat (Triticum aestivum L.) Using 90K SNP Array

“…Further studies may still be needed to determine the key factors affecting the accuracy of consensus map construction and subsequent QTL mapping, such as proportion of common markers shared by multiple mapping populations, inconsistency degree of marker orders in individual populations, population-specific recombination frequencies, and the optimum algorithm used to construct the consensus map. In addition to bi-parental populations, as have been used in this study, multi-parental populations have been developed in recent years in crops together with suitable genetic analysis methods (Gardner et al, 2016 ; Zhang et al, 2017 , 2019 ; Shi et al, 2019 ; Qu et al, 2020 ). In theory, a consensus map can also be constructed by combining a number of bi-parental and multi-parental populations, when common markers are shared by these populations.…”

Sparse Phenotyping and Haplotype-Based Models for Genomic Prediction in Rice

“…The third population is provided by Meng et al ( 2016 ) and Qu et al ( 2020 ) comprising 1048 recombinant inbred lines (RILs) originating from eight genetically distant Indica lines. These RILs were phenotypically evaluated for DTH and PH in DS and WS of year 2014 in International Rice Research Institute (IRRI) and two locations in China, namely Jiangxi (JX) and Shenzhen (SZ), in year 2016.…”

“…The combination of season/location and year was regarded as the environment, thereupon phenotypic data of four environments was available for the 1048 RILs. These RILs were fingerprinted by a customized rice 55 K SNP array (Qu et al 2020 ). After assigning all heterozygous SNP scores to missing data and the quality control of removing SNPs with minor allele frequency less than 0.05 or missing rate greater than 0.1, 33,518 SNPs were available for the 1048 RILs.…”

QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice

“…A NAM population is usually generated by crossing multiple genotypes with a single genotype. Using multiparental population for QTL mapping provides an opportunity to test pleiotropy, genetic background effect, and the genetic overlap between different complex traits (Qu et al, 2020). Buckler et al (2009) developed a NAM population that was consisted of 25 families with 200 lines per family in maize.…”