Abstract
Key messageA 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 F2 populations 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.
Highlights
As for the grain width (GW), Percentage of grains with chalkiness (PGWC), and degree of endosperm chalkiness (DEC), the averaged values of 2.9 mm, 18.5%, and 5.8% were detected for the Minghui 63 (MH63)-introgression lines (ILs) but the ones of 3.3 mm, 74.9%, and 46.5% were detected for the 02428-ILs
It is notable that the PGWC and DEC showed much larger variations than the grain shape traits (Table 1)
A total of 41 and 30 QTL for appearance quality (AQ) traits were identified across five environments in the two sets of ILs derived from MH63 and 02428 (Table 3; Fig. 2), respectively
Summary
With the economy development of rice-consuming area, grain quality especially the appearance quality (AQ) is being attracted more attention by both consumers and producers than ever before. It has become one key target trait equivalent to the grain yield in the rice breeding program (Tan et al 2000). Rice AQ consists of grain shape and grain chalkiness. Different shapes of grains (de-hulled seeds) have different market values in different areas (Luo et al 2004). AQ traits have become more and more important in breeding schemes in rice producing areas around the world, especially for hybrid rice in China (Tan et al 2000)
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