Identification of rice chromosome segment substitution Line Z747 with increased grain number and QTL mapping for related traits

Abstract

Increasing grain number per panicle is important for rice breeding for high yield. Its inheritance is very complex and controlled by many genes. Chromosome segment substitution lines can dissect complex traits controlled by many genes, and thus are ideal genetic research materials. Here, an excellent rice chromosome segment substitution line Z747 with increased grain number was identified from recipient Nipponbare and donor Xihui 18 through advanced backcrossing and inbreeding combined SSR marker-assisted selection. Z747 carried fifteen substitution segments with 4.49 Mb of average length. Compared with Nipponbare, Z747 had significantly increased spikelet number per panicle, number of primary branches, number of secondary branches, panicle length and grain length, and decreased grain width and seed setting rate. However, the seed setting rate in Z747 was still up to 81%. Furthermore, secondary F2 population from crosses between Nipponbare and Z747 was used to map QTL for related traits. A total of 46 QTLs distributed on chromosomes 1, 2, 3, 5, 6, 9, 11, and 12 were detected. Among them, 12 QTLs such as qGPP12 , qPH-3-1 , and qPH-3-2 etc. might be alleles of cloned genes, and the remaining 34 QTLs such as qSPP9 etc. might not be identified in the past. The spikelet number per panicle of Z747 was mainly controlled by two QTLs ( qSPP3 and qSPP5 ) with effects of increasing spikelet number and one ( qSPP9 ) with decreasing effects. These results are important for fine mapping and cloning of major QTL, and developing single-segment substitution lines carrying favorable QTLs.