Abstract
BackgroundWith an increasing world population and a gradual decline in the amount of arable land, food security remains a global challenge. Continued increases in rice yield will be required to break through the barriers to grain output. In order to transition from hybrid rice to super-hybrid rice, breeding demands cannot be addressed through traditional heterosis. Therefore, it is necessary to incorporate high yield loci from other rice genetic groups and to scientifically utilize intersubspecific heterosis in breeding lines. In this study, 781 lines from a segregating F2 population constructed by crossing the indica variety, “Giant Spike Rice” R1128 as trait donor with the japonica cultivar ‘Nipponbare’, were re-sequenced using high-throughout multiplexed shotgun genotyping (MSG) technology. In combination with high-density single nucleotide polymorphisms, quantitative trait locus (QTL) mapping and genetic effect analysis were performed for five yield factors (spikelet number per panicle, primary branches per panicle, secondary branches per panicle, plant height, and panicle length) to explore the genetic mechanisms underlying the formation of the giant panicle of R1128. Also, they were preformed to locate new high-yielding rice genetic intervals, providing data for super-high-yielding rice breeding.ResultsQTL mapping and genetic effect analysis for five yield factors in the population gave the following results: 49 QTLs for the five yield factors were distributed on 11 of 12 chromosomes. The super-hybrid line R1128 carries multiple major genes for good traits, including Sd1 for plant height, Hd1 and Ehd1 for heading date, Gn1a for spikelet number and IPA1 for ideal plant shape. These genes accounted for 44.3%, 21.9%, 6.2%, 12.9% and 10.6% of the phenotypic variation in the individual traits. Six novel QTLs, qph1-2, qph9-1, qpl12-1, qgn3-1, qgn11-1 and qsbn11-1 are reported here for the first time.ConclusionsHigh-throughout sequencing technology makes it convenient to study rice genomics and makes the QTL/gene mapping direct, efficient, and more reliable. The genetic regions discovered in this study will be valuable for breeding in rice varieties because of the diverse genetic backgrounds of the rice.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-21) contains supplementary material, which is available to authorized users.
Highlights
With an increasing world population and a gradual decline in the amount of arable land, food security remains a global challenge
Previous studies have demonstrated that plant height, panicle length, heading date and flag leaf length present a significant positive correlation; multiple quantitative trait locus (QTL) are mapped to the same area, such as plant height and spike length. This indicates that the relationship among the quantitative traits is extremely intricate; the functional direction does not change (Zhang et al 2006). This study revealed such cases: (Ping et al 2003) mapped qph-2 between 5263536 and 30654749 bp on chromosome 2 with 81 indica-japonica DH populations. qpl2-1 that controls panicle length in this paper falls within this interval; qph3-1 and qph3-2 mapped for PH characteristics that are linked to bin1846 and bin1943 for main PL when their positive alleles are derived from the Nipponbare parent with positive effects
Multiple sequencing was preformed by using multiplexed shotgun genotyping (MSG) sequencing technology, while QTLs linked to agronomic traits were mapped and analyzed for their effect
Summary
With an increasing world population and a gradual decline in the amount of arable land, food security remains a global challenge. It is necessary to pursue a higher level of heterosis by using the genetic differences that exist in more distantly-related rice germplasm (subspecies, interspecific and intergeneric) in order to break through the bottleneck in traditional rice heterotic hybrid approaches, to maximally exploit the interaction potential of rice yield genes (additive, dominance, over-dominance and epistasis). This can be used to help breed super-hybrid rice parental lines, and to accelerate the steps required for super-hybrid rice breeding (Deng et al 2010)
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