Abstract
Single segment substitution lines (SSSLs) have been confirmed to be powerful tools to perform quantitative trait locus (QTL) analysis. This study illuminated the process and methods of QTL analysis with SSSLs on heading date (HD) in rice. QTL identification under two cropping seasons revealed 98 of 202 SSSLs associated with HD. A total of 22 QTLs were positioned in relative narrow regions on chromosomes by mrMLM.GUI software. QTL qHd3-1 was precisely positioned at 4.4 cM on chromosome 3 by a secondary F2 population. Through SSSL pyramiding, double segment substitution lines were constructed and used to analyze epistatic interactions of digenic loci. Epistatic effects for three pairs of QTLs were estimated, indicating the interactions of QTL qHd3-1 with other QTLs detected and the role to enhance the expression of early ripening or restraining of late flowering QTLs. Additionally, analysis of QTL in different environments provided information about the stability of HD QTLs. This type of research points out the way to excavate favorable genes for design breeding.
Highlights
Heading date (HD) is a key agronomical determinant for current varieties of cultivated rice to adapt to specific cultivation regions and cropping seasons[1]
Some segment substitution lines (SSSLs) were selected as experimental materials to develop secondary populations such as F2 for quantitative trait locus (QTL) fine mapping and to aggregate SSSLs for epistatic analysis[8,17,18,19,20,21,22] and design breeding[14]
This paper took data of heading date (HD) evaluated from two cropping seasons in 2016 as an example to explain the process and validity of QTL analysis via SSSLs
Summary
Heading date (HD) is a key agronomical determinant for current varieties of cultivated rice to adapt to specific cultivation regions and cropping seasons[1]. By conventional mapping populations, such as mainly F2s, BC1F1s, RILs (recombinant inbred lines) or DHLs (doubled haploid lines), QTLs contributing to heading date in Oryza species had been intensively explored and mapped to their residing chromosomal regions[2,4] These populations, in which multiple genetic factors on the whole genome segregate simultaneously, cannot be used as the materials for the precise mapping of QTLs. it would be more difficult to determinate the true genetic actions of the QTLs and to differentiate QTL effects from background noise[5,6]. Near-isogenic lines (NILs) developed by sequential backcrossing were widely used to accurate genetic analysis of genes because the NILs populations made the genetic background consistent[6,7] This type of populations has been employed for QTL analysis on numerous traits in various crops. Epistatic analysis between QTLs was well done via analysis of aggregation lines of SSSLs10
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