Backcross Inbred Line Population Research Articles

Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum).

Integrated QTL mapping and WGCNA condense the potential gene regulatory network involved in oil accumulation. A glycosyl hydrolases gene (GhHSD1) for oil biosynthesis was confirmed in Arabidopsis, which will provide useful knowledge to understand the functional mechanism of oil biosynthesis in cotton. Cotton is an economical source of edible oil for the food industry. The genetic mechanism that regulates oil biosynthesis in cottonseeds is essential for the genetic enhancement of oil content (OC). To explore the functional genomics of OC, this study utilized an interspecific backcross inbred line population to dissect the quantitative trait locus (QTL) interlinked with OC. In total, nine OC QTLs were identified, four of which were novel, and each QTL explained 3.62-34.73% of the phenotypic variation of OC. The comprehensive transcript profiling of developing cottonseeds revealed 3,646 core genes differentially expressed in both inbred parents. Functional enrichment analysis determined 43 genes were annotated with oil biosynthesis processes. Implementation of weighted gene co-expression network analysis showed that 803 differential genes had a significant correlation with the OC phenotype. Further integrated analysis identified seven important genes located in OC QTLs. Of which, the GhHSD1 gene located in stable QTL qOC-Dt3-1 exhibited the highest functional linkages with the other network genes. Phylogenetic analysis showed significant evolutionary differences in the HSD1 sequences between oilseed- and starch- crops. Furthermore, the overexpression of GhHSD1 in Arabidopsis yielded almost 6.78% higher seed oil. This study not only uncovers important genetic loci for oil accumulation in cottonseed, but also provides a set of new candidate genes that potentially influence the oil biosynthesis pathway in cottonseed.

Resequencing-based QTL mapping for yield and resistance traits reveals great potential of Oryza longistaminata in rice breeding

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC2F20 backcross inbred line (BIL) population of 152 lines from the cross of 9311 × O. longistaminat. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13 QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species. A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and 27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement.

Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense.

Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91–35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.

Quantitative Trait Locus Mapping of Salt Tolerance in Wild Rice Oryza longistaminata.

Salt stress is one of the most severe adverse environments in rice production; increasing salinization is seriously endangering rice production around the world. In this study, a rice backcross inbred line (BIL) population derived from the cross of 9311 and wild rice Oryza longistaminata was employed to identify the favorable genetic loci of O. longistaminata for salt tolerance. A total of 27 quantitative trait loci (QTLs) related to salt tolerance were identified in 140 rice BILs, and 17 QTLs formed seven QTL clusters on different chromosomes, of which 18 QTLs were derived from O. longistaminata, and a QTL for salt injury score (SIS), water content of seedlings (WCS) under salt treatment, and relative water content of seedlings (RWCS) was repeatedly detected and colocalized at the same site on chromosome 2, and a cytochrome P450 86B1 (MH02t0466900) was suggested as the potential candidate gene responsible for the salt tolerance based on sequence and expression analysis. These findings laid the foundation for further improving rice salt tolerance through molecular breeding in the future.

Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines.

Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota “Songzi” and the orange cultivar “Amsterdam forcing” was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC2F1 plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4–66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.

Mapping of dynamic QTLs for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a backcross inbred line population of Upland cotton.

A backcross inbred line population of cotton was evaluated for Fusarium wilt race 4 resistance at different days after inoculation (DAI). Both constitutively expressed and developmentally regulated QTLs were detected. The soil-borne fungus Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) causes Fusarium wilt including seedling mortality in cotton. A backcross inbred line (BIL) population of 181 lines, derived from a bi-parental cross of moderately resistant non-recurrent Hai 7124 (Gossypium barbadense) and recurrent parent CCRI 36 (G. hirsutum), was evaluated under temperature-controlled conditions for FOV4 resistance with artificial inoculations. Based on three replicated tests evaluated at 7, 14, 21, and 28days after inoculation (DAI), only 2-5 BILs showed lower disease severity ratings (DSR) than the parents while 22-50 BILs were more susceptible, indicating transgressive segregation toward susceptibility. Although DSR were overall congruent between DAI, there were many BILs displaying different responses to FOV4 across DAI. Genetic mapping using 7709 SNP markers identified 42 unique QTLs for four evaluation parameters- disease incidence (DI), DSR, mortality rate (MR), and area under disease progress curve (AUDPC), including 26 for two or more parameters. All five QTLs for AUDPC were co-localized with QTLs for DI, DSR, and/or MR at one or two DAI, indicating the unnecessary use of AUDPC in QTL mapping for FOV4 resistance. Those common QTLs explained the significant positive associations between parameters observed. Ten common QTLs with negative or positive additive effects were detected between DAI. DAI-specific and consistent QTLs were detected between DAI in cotton for the first time, suggesting the existence of both constitutively expressed and developmentally regulated QTLs for FOV4 resistance and the importance of evaluating genetic populations for FOV4 resistance at different growth stages.

Identification of QTLs for Salt Tolerance at the Germination and Seedling Stages in Rice.

Rice is highly sensitive to salinity stress during the seedling establishment phase. Salt stress is widely occurring in cultivated areas and severely affects seed germination ability and seedling establishment, which may result in a complete crop failure. The objective of the present study is to identify quantitative trait loci (QTLs) related to salt tolerance of the germination and seedling stages in a rice backcross inbred line (BIL) population that was derived from a backcross of an Africa rice ACC9 as donor and indica cultivar Zhenshan97 (ZS97) as the recurrent parent. Under salt stress, ACC9 exhibited a higher germination percentage, but more repressed seedling growth than ZS97. Using the BIL population, 23 loci for germination parameters were detected at the germination stage and 46 loci were identified for several morphological and physiological parameters at the seedling stage. Among them, nine and 33 loci with the ACC9 alleles increased salt tolerance at the germination and seedling stages, respectively. Moreover, several major QTLs were found to be co-localized in the same or overlapping regions of previously reported genes for salt stress. These major loci will facilitate improving salt-tolerance rice in genome-breeding programs.

Genetic variability, Genotype × Environment interaction for grain yield of wheat (Triticum aestivum) backcross inbred lines population under different moisture regimes

Drought stress is well known phenomenon that affects the productivity of wheat (Triticum aestivum L). Knowledge on genetic variation, genotype × environment interaction and association between physiological and yield component traits is crucial for the development of improved varieties having high yield and water use efficiency. The present study consists of 280 backcross inbred lines (BILs) population evaluated for grain yield and morpho-physiological traits for two years at three locations. Combined ANOVA unfolded significant variability among traits in BILs population for yield and morpho-physiological traits.Grain yield showed significant association with normalized difference vegetation index (NDVI), soil plant analysis development (SPAD), thousand grain weight (TGW), and canopy temperature (CT). The genotype, environment and genotype ×environment interaction for yield was highly significant (p< 0.01). ASV (AMMI stability value) was calculated and top 29 genotypes were selected and further analyzed with AMMI and GGE biplot analysis for dissecting out genotype × environment interaction. The results classified genotypes G82, G202, G234, G263, G6, G192 and G77 are most stable and high yielding genotypes.

Genetic Dissection and Validation of Chromosomal Regions for Transmission Ratio Distortion in Intersubspecific Crosses of Rice.

Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of a reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare (NIP) and an indica variety 9311 was utilized to study the genetic base of TRD. A total of 18 genomic regions were identified for TRD in the BILs. Among them, 12 and 6 regions showed indica (9311) and japonica (NIP) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from intersubspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intrasubspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking intersubspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the intersubspecific hybrid breeding programs.

Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

BackgroundSeed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown.ResultsQuantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome segment substitution line (CSSL) and backcross inbred line (BIL) population, both derived from the same parents Nipponbare, a japonica cultivar with seed dormancy, and 9311, an indica cultivar lacking seed dormancy. A total of 12 and 27 QTL regions for seed dormancy were detected in the CSSLs and BILs, respectively. Among these regions, four major loci (qSD3.1, qSD3.2, qSD5.2 and qSD11.2) were commonly identified for multiple germination parameters associated with seed dormancy in both populations, with Nipponbare alleles delaying the seed germination percentage and decreasing germination uniformity. Two loci (qSD3.1 and qSD3.2) were individually validated in the near-isogenic lines containing the QTL of interest. The effect of qSD3.2 was further confirmed in a CSSL-derived F2 population. Furthermore, both qSD3.1 and qSD3.2 were sensitive to abscisic acid and exhibited a significant epistatic interaction to increase seed dormancy.ConclusionsOur results indicate that the integration of the developed CSSLs and BILs with high-density markers can provide a powerful tool for dissecting the genetic basis of seed dormancy in rice. Our findings regarding the major loci and their interactions with several promising candidate genes that are induced by abscisic acid and specifically expressed in the seeds will facilitate further gene discovery and a better understanding of the genetic and molecular mechanisms of seed dormancy for improving seed quality in rice breeding programs.

Quantitative trait loci analysis of seed-specialized metabolites reveals seed-specific flavonols and differential regulation of glycoalkaloid content in tomato.

Given the potential health benefits (and adverse effects), of polyphenolic and steroidal glycoalkaloids in the diet there is a growing interest in fully elucidating the genetic control of their levels in foodstuffs. Here we carried out profiling of the specialized metabolites in the seeds of the Solanum pennellii introgression lines identifying 338 putative metabolite quantitative trait loci (mQTL) for flavonoids, steroidal glycoalkaloids and further specialized metabolites. Two putative mQTL for flavonols and one for steroidal glycoalkaloids were cross-validated by evaluation of the metabolite content of recombinants harboring smaller introgression in the corresponding QTL interval or by analysis of lines from an independently derived backcross inbred line population. The steroidal glycoalkaloid mQTL was localized to a chromosomal region spanning 14 genes, including a previously defined steroidal glycoalkaloid gene cluster. The flavonoid mQTL was further validated via the use of transient and stable overexpression of the Solyc12g098600 and Solyc12g096870 genes, which encode seed-specific uridine 5'-diphosphate-glycosyltransferases. The results are discussed in the context of our understanding of the accumulation of polyphenols and steroidal glycoalkaloids, and how this knowledge may be incorporated into breeding strategies aimed at improving nutritional aspects of plants as well as in fortifying them against abiotic stress.

Genetic analysis of germinating ability under alkaline and neutral salt stress by a high-density bin genetic map in rice

The knowledge about the genetic basis of alkaline salt stress and neutral salt stress in rice is limited. Here, we located quantitative trait loci (QTL) for seed germination rate (GR) under alkaline salt stress (NaHCO3) and neutral salt stress (NaCl) using backcross inbred lines population, which was derived from a cross between indica cv. Changhui 891 (CH891) and japonica cv. 02428 with 3057 bins markers. A total of ten QTL for five salt stress-related traits were detected. The QTL detected for control condition, NaCl stress, and NaHCO3 stress were quite different, which suggested that the genes controlling the transport of the Na+, in the form of NaCl and the NaHCO3, may be different or induced incoordinately by salt stress. Furthermore, on the basis of the high-density genetic map, the ten QTL were mapped on 40–980 kb chromosomal regions on Nipponbare genome, and 16 candidate genes related to stress or metal transport were found. These results contribute to the fine mapping and use of these GR-related QTL.

Effects of drought on agronomic and fiber quality in an introgressed backcross inbred line population of Upland cotton under field conditions

Upland cotton (Gossypium hirsutum) is the most important fiber crop and an important oilseed crop in the world. Developing drought tolerant cultivars is important to sustainable cotton production in arid and semi-arid regions. However, there is a lack of information on genetic variation for drought tolerance in breeding populations. In this study, a backcross inbred line (BIL) Upland population with germplasm introgression from a more drought-tolerant American Pima cotton (G. barbadense) parent was evaluated in multiple field environments under well-watered (WW) and water-limited (WL) conditions at the flowering stage. Drought at the flowering stage reduced seedcotton yield (SCY), lint yield (LY), boll weight (BW), fiber length (FL), and fiber strength (STR) but increased lint percentage (LP), micronaire (MIC), neps per size, nep per gram, seedcoat nep size, and seed coat fragment count by gram. Significant genetic differences in the BIL population were detected for most agronomic and fiber quality traits and drought susceptibility index (DSI) for these traits. DSI of SCY and LY ranged from 0.01 to 1.5 and 0.1–1.45, respectively, reflecting the tolerance level of the BILs under WL conditions. The broad-sense heritability estimates were moderate for most agronomic traits and moderate to high for most fiber quality traits. Results indicated that highly positive correlation was detected for agronomic and fiber quality traits between WW and WL conditions, with the highest correlations for SCY, LY, UHM, SCY, and MIC. Promising BILs with drought tolerance were identified. This study has provided a line of evidence that field drought tolerance was transferred from the more drought tolerant Pima line to Upland cotton.

Genetic gain and morpho-physiological characterisation of BILs (Backcross inbred lines) under different moisture regimes in wheat (Triticum aestivum. L)

Drought stress is one of the major yield limiting factors in realising the full genetic potential of wheat. In the present study, backcross inbred line population derived from GW322*2/ HI1500 was characterized for different morpho-physiological traits and grain yield under rainfed and irrigated conditions. Principal component analysis revealed that first five components explained over 66.35 per cent of variation. Grain yield showed significant correlation with biomass and physiological traits viz., NDVI2, NDVI3, NDVI5, CT2, CT3 and CT4. The analysis of variance on grain yield data showed that mean squares of environments, genotypes and GEI were highly significant (p 0.01). To determine effects of GEI on grain yield, data were subjected to AMMI and GGE biplot analysis, which identified BILs G20, G2, G254, G214, G44 and G64 as the most stable and high yielding. Based on Smith selection index expected genetic gain for grain yield at 5% was 131.01gm/plot. Hence, selecting genotypes based on morpho-physiological traits will be rewarding under moisture depleting environment.

Wide crossing diversify mitogenomes of rice

BackgroundIn most angiosperms, the inheritance of the mitochondria takes place in a typical maternal manner. However, very less information is available about if the existence of structural variations or not in mitochondrial genomes (mitogenomes) between maternal parents and their progenies.ResultsIn order to find the answer, a stable rice backcross inbred line (BIL) population was derived from the crosses of Oryza glaberrima/Oryza sativa//Oryza sativa. The current study presents a comparative analysis of the mitogenomes between maternal parents and five BILs. There were recorded universal structural variations such as reversal, translocation, fusion, and fission among the BILs. The repeat-mediated recombination and non-homologous end-joining contributed virtually equal to the rearrangement of mitogenomes. Similarly, the relative order, copy-number, expression level, and RNA-editing rate of mitochondrial genes were also extensively varied among BILs.ConclusionsThese novel findings unraveled an unusual mystery of the maternal inheritance and possible cause for heterogeneity of mitogenomes in rice population. The current piece of work will greatly develop our understanding of the plant nucleo-cytoplasmic interaction and their potential role in plant growth and developmental processes.

Characterizing the main and epistatic effects and interactions of germination-related quantitative trait loci of tomato using a backcross inbred line population and near-isogenic lines

Rapid germination and early establishment of seedlings under unfavorable environmental conditions are desirable traits for seedling production. Quantitative trait locus (QTL) analysis of germination speed was conducted at 15 and 25 °C using a backcross inbred line family. Final germination percentage (FGP), days to 50 % and 90 % of FGP (GT50 and GT90, respectively), mean germination time (MGT), and covariance of germination time were determined. The results indicated 11 additive germination-related QTLs on chromosomes 1–3, and 11. GT50, GT90, and MGT QTLs detected on chromosomes 1–3 were co-located, of which, gt501, gt901, and mgt1 had positive additive effects. A single epistatic QTL was detected, but no QTL with additive effect was found on chromosome 4 in the present study, which was not consistent with the results of previous studies. To reexamine the effect of QTLs on chromosomes 1 and 4, we constructed one and three near-isogenic lines (NILs) carrying a substituted chromosome segment from Solanum pimpinellifolium (SP) in which putative QTLs were detected on chromosomes 1 and 4. NIL experiment results indicated that a chromosomal segment from SP between TGS0308 and C2_At5g49480 markers on chromosome 1 shortened and prolonged germination time at 15 °C and 25 °C, respectively, due to QTL-by-environmental interactions. However, the substituted segment between SSR603 and TGS0411 markers on chromosome 4 did not affect seed germination. In conclusion, the QTL on chromosome 1 is useful for breeding cultivars that are able to germinate at low temperatures.

Identification of favorable alleles for rice seedling anoxic tolerance using natural and bi-parental populations

The acreage of submerged direct-sown cultivation of Oryza sativa is gradually increasing in China because of the constantly decreasing number of laborers in rural areas. Identifying favorable alleles for seedling anoxic tolerance (SAT) is necessary for improving cultivars suitable for submerged direct-sown rice cultivation. In this study, we used two populations to detect quantitative trait loci (QTLs) for SAT. In the natural population consisting of 542 accessions, seven simple sequence repeat marker loci associated with SAT were detected in both 2016 and 2017, with 22 favorable alleles. RM5340 on chromosome 2 and RM6811 on chromosome 6 were newly identified. Allele RM6811-160 bp had the largest phenotypic effect (1.09 cm/cm). Seventy-one accessions carried this allele. In the backcross inbred line population (115 lines) derived from Wuyunjing 7 hao/Ludao//Wuyunjing 7 hao, 8 QTLs for SAT were detected, with the phenotypic variance explained (PVE) ranging from 2.51 to 12.11%. The qCELpc2, qCELpc3, qCELpc5 and qCELpc11 loci were newly detected. The favorable alleles of loci qCELpc3, qCELpc5 and qCELpc11 were from Ludao. The locus qCELpc11 had the largest PVE of 10.39%, with a substitutive effect of 0.82 cm averaged over 2 years. By sequencing the gene locus OsBIERF, which was within a 15.50–16.08 Mb chromosome region harboring SAT-associated RM3600 on chromosome 9 and was detected in both populations, a single nucleotide polymorphism locus at the first exon was found between Wuyunjing 7 hao (T) and Ludao (C). The favorable alleles detected in this study could be used to improve SAT of rice cultivars.

QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense.

We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencingfor QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24cM with a mean marker interval of 0.67cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.

Updating the Genome of the Elite Rice Variety Kongyu131 to Expand Its Ecological Adaptation Region.

As an elite rice variety cultivated in the third accumulative temperature belt in Heilongjiang province, China, Kongyu131 has many excellent traits, such as high quality, high stability, early maturation and cold resistance. However, as with other crop varieties, Kongyu131 has regional restrictions, exhibiting decreased yields when grown at low latitudes. To address these problems, two populations were constructed from cross between japonica and indica varieties. QTL analyses were performed with these two populations to detect regional adaptation related quantitative trait locus. Results in a BC1F6 backcross inbred line population with 168 lines derived from cross between Kongyu131 and GKMP showed a large pleiotropic QTL near 9 Mb on chromosome 7, which significantly delayed the HD of Kongyu131 and increased the plant height (PH), length of main panicle (LMP), number of primary branches (NPB) and grain number of main panicles (GNP). We also found a similar QTL in the population BC3F2 derived from Kongyu131 and GKLPL. Based on the QTL, we developed a gene module named mRA7 with 5 single-nucleotide polymorphism (SNP) markers around the QTL. Through a foreground and background selection based on 197 SNP markers evenly distributed over the 12 chromosomes, we obtained a new plant (a single point substitution line, SPSL) with a new Kongyu131 genome, carrying only a small chromosomal fragment less than 800 kb from GKLPL. The background recovery ratio of the SPSL was 99.8%. Compared with Kongyu131, the SPSL exhibited a significant HD delay of approximately 31 days and increased PH, LMP and GNP values when planted in Heilongjiang province. When cultivated in Guangdong province, HD of SPSL showed only 16 days delay, and less increase in PH, LMP and GNP than in Heilongjiang province. Phenotypic evaluation showed that the SPSL could be moved to south by more than 3 latitude units and cultivated in low-latitude regions. This study exemplifies the feasibility of expanding the regions of cultivation of elite rice varieties via similar methods.

Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton.

Fiber length is one of the most important fiber quality traits in Upland cotton (Gossypium hirsutum L.), the most important fiber crop, and its improvement has been impeded in part by a lack of knowledge regarding its genetic basis. Introgressed backcross inbred lines (BILs) or near isogenic lines (NILs) differing in fiber length in the same genetic background, developed through advanced backcrossing between Upland cotton and extra-long staple cotton (G. barbadense L.), provide an important genomic resource for studying the molecular genetic basis of fiber length. In the present study, a long-fiber group and a short-fiber group, each with five BILs of Upland cotton, were selected from a BIL population between G. hirsutum and G. barbadense. Through amicroarray-based comparative transcriptome analysis of developing fibers at 10 days postanthesis from the two groups, 1478 differentially expressed genes (DEGs) were identified. A total of 166 DEGs were then mapped to regions of fiber length quantitative trait loci (QTL), including 12 QTL hotspots and 2 QTL identified previously in the BIL population from which the two sets of BILs were selected. Several candidate genes possibly underlying the genetic control of fiber length differences between G. barbadense and G. hirsutum, including GhACX and GhKIF, were identified in this study. These results provide a list of positional candidate genes for the fine-scale mapping and map-based cloning of fiber length QTL, which will facilitate targeted gene transfer from G. barbadense to Upland cotton to further improve fiber quality.