Genome-wide recombination variation in biparental segregating and reciprocal backcross populations provides information for introgression breeding in Brassica napus

Variation in patterns of recombination in plant genomes provides information about species evolution,genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed(Brassica napus)(AACC, 2n = 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93%of the genome contained crossovers at a mean rate of 3.8 c M Mb^(-1), with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

Background:Genetic improvement in fiber quality is one of the main challenges for cotton breeders.Quantitative trait loci(QTL)mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits.In present study,F14 recombinant inbred line(RIL)population was backcrossed to paternal parent for a paternal backcross(BC/P)population,deriving from one upland cotton hybrid.Three repetitive BC/P field trials and one maternal backcross(BC/M)field trial were performed including both two BC populations and the original RIL population.Results:In total,24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results.Thirty-five QTLs in BC/P populations explain 5.01%–22.09%of phenotype variation(PV).Among the 35 QTLs,23 QTLs are detected in BC/P population alone.Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects.Particularly,qFS-Chr3–1 explains 22.09%of PV in BC/P population,which increaseds 0.48 cN·tex−1 for fiber strength.A total of 7,2,8,2 and 6 QTLs explain over 10.00%of PV for fiber length,fiber uniformity,fiber strength,fiber elongation and fiber micronaire,respectively.In RIL population,six common QTLs are detected in more than one environment:qFL-Chr1–2,qFS-Chr5–1,qFS-Chr9–1,qFS-Chr21–1,qFM-Chr9–1 and qFM-Chr9–2.Two common QTLs of qFE-Chr2–2(TMB2386-SWU12343)and qFM-Chr9–1(NAU2873-CGR6771)explain 22.42%and 21.91%of PV.The region between NAU4034 and TMB1296 harbor 30 genes(379 kb)in A05 and 42 genes(49 kb)in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population,respectively.In addition,a total of 142 and 46 epistatic QTLs and QTL×environments(E-QTLs and QQEs)are identified in recombinant inbred lines in paternal backcross(RIL-P)and paternal backcross(BC/P)populations,respectively.Conclusions:The present studies provide informative basis for improving cotton fiber quality in different populations.

Genetic Analysis of Cold Tolerance at Seedling Stage and Heat Tolerance at Anthesis in Rice (Oryza sativa L.)

A set of 240 introgression lines derived from the advanced backcross population of a cross between a japonica cultivar,Xiushui 09,and an indica breeding line,IR2061,was developed to dissect QTLs affecting cold tolerance （CT） at seedling stage and heat tolerance （HT） at anthesis.Survival rate of seedlings （SRS） and spikelet fertility （SF）,the index traits of CT and HT,showed significant differences between the two parents under stresses.A total of four QTLs （qSRS1,qSRS7,qSRS11a and qSRS11b） for CT were identified on chromosomes 1,7,11,and the Xiushui 09 alleles increased SRS at all loci except qSRS7.Four QTLs for SF were identified on chromosomes 4,5,6,and 11.These QTLs could be classified into two major types based on their behaviors under normal and stress conditions.The first was QTL expressed only under normal condition;and the second QTL was apparently stress induced and only expressed under stress.Among them,two QTLs （qSF4 and qSF6） which reduced the trait difference between heat stress and normal conditions must have contributed to HT because of their obvious contribution to trait stability,and the IR2061 allele at the qSF6 and the Xiushui 09 allele at the qSF4 improved HT,respectively.No similar QTL was found between CT at seedling stage and HT at anthesis.Therefore,it is possible to breed a new variety with CT and HT by pyramiding the favorable CT-and HT-improved alleles at above loci from Xiushui 09 and IR2061,respectively,through marker-assisted selection （MAS）.

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.)

Using an accession of common wild rice （Oryza rufipogon Griff.） collected from Yuanjiang County, Yunnan Province, China, as the donor and an elite cultivar 93-11, widely used in two-line indica hybrid rice production in China, as the recurrent parent, an advanced backcross populations were developed. Through genotyping of 187 SSR markers and investigation of six yield-related traits of two gen- erations （BC4F2 and BC4F4）, a total of 26 QTLs were detected by employing single point analysis and interval mapping in both genera-tions. Of the 26 QTLs, the alleles of 10 （38.5%） QTLs originating from O. rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background. In addition, five QTLs controlling yield and its components were newly identified, indicating that there are potentially novel alleles in Yuanjiang common wild rice. Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1, 7 and 12. The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation, suggesting the pleiotropism or tight linkage. Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.