Backcross Inbred Lines Research Articles

Genetic analysis of fruit quality traits in prebred lines of watermelon derived from a wild accession of Citrullus amarus

Citron (Citrullus amarus) is a watermelon (Citrullus lanatus) relative that is reported to carry disease resistance alleles to several important pathogens. It is therefore important to understand the inheritance of fruit quality traits while using this species to introgress resistance traits. Hence, the current experiment was carried out to determine the inheritance of important external and internal fruit quality traits in prebred lines derived from C. amarus and confirm the role of candidate genes for quality traits in these genotypes. The study comprised of two backcross inbred lines viz, BIL-53 and BIL-99 as female parents crossed to IIHR-140-152, an icebox type elite inbred line as a common pollen parent for developing F1, F2, BC1 and BC2 generations to study genetics of fruit shape, flesh color, rind pattern, total soluble solids (TSS), and seed color. Results suggested that the genetics of most of these fruit quality traits are governed by one or two genes suggesting simple inheritance. Sequencing of candidate gene, Cla011257 confirmed its involvement for fruit shape in this species and also revealed a novel allele with two SNPs resulting in oblong fruit shape. Similarly, the flesh color candidate gene, LCYB was involved in variation between canary yellow and red flesh colors but was found to be not involved in salmon yellow color observed in progenies derived from this species. Overall, our results suggest that breeders can use C. amarus as a source of resistance in breeding programs without linkage drag of alleles detrimental for fruit quality traits.

Analysis of the MIR160 gene family and the role of MIR160a_A05 in regulating fiber length in cotton

Main conclusionThe MIR160 family in Gossypium hirsutum and G. barbadense was characterized, and miR160a_A05 was found to increase cotton-fiber length by downregulating its target gene (ARF17) and several GH3 genes.Cotton fiber is the most important raw material for the textile industry. MicroRNAs are involved in regulating cotton-fiber development, but a role in fiber elongation has not been demonstrated. In this study, miR160a was found to be differentially expressed in elongating fibers between two interspecific (between Gossypium hirsutum and G. barbadense) backcross inbred lines (BILs) with different fiber lengths. The gene MIR160 colocalized with a previously mapped fiber-length quantitative trait locus. Its target gene ARF17 was differentially expressed between the two BILs during fiber elongation, but in the inverse fashion. Bioinformatics was used to analyze the MIR160 family in both G. hirsutum and G. barbadense. Moreover, qRT–PCR analysis identified MIR160a as the functional MIR160 gene encoding the miR160a precursor during fiber elongation. Using virus-induced gene silencing and overexpression, overexpressed MIR160a_A05 resulted in significantly longer fibers compared with wild type, whereas suppression of miR160 resulted in significantly shorter fibers. Expression levels of the target gene auxin-response factor 17 (ARF17) and related genes GH3 in the two BILs and/or the virus-infected plants demonstrated similar changes in response to modulation of miR160a level. Finally, overexpression or suppression of miR160 increased or decreased, respectively, the cellular level of indole-3-acetic acid, which is involved in fiber elongation. These results describe a specific regulatory mechanism for fiber elongation in cotton that can be utilized for future crop improvement.

A genome-wide analysis of pentatricopeptide repeat (PPR) protein-encoding genes in four Gossypium species with an emphasis on their expression in floral buds, ovules, and fibers in upland cotton.

Cotton is the most important natural fiber used in textiles. Breeding for "three-lines", i.e., cytoplasmic male sterility (CMS)-based sterile (A), maintainer (B), and restorer (R) line, is a promising approach to harness hybrid vigor in cotton. Pentatricopeptide repeat (PPR) protein-encoding genes play an important role in plant growth and development including restoration of CMS plants to male fertility. However, PPRs, especially those contributing to CMS and fiber development, remain largely unknown in cotton. In this study, a genome-wide identification and characterization of PPR gene family in four Gossypium species with genome sequences (G. arboreum, G. raimondii, G. hirsutum, and G. barbadense) were performed, and expressed PPR genes in developing floral buds, ovules, and fibers were compared to identify possible PPRs related to CMS restoration and fiber development. A total of 539, 558, 1032, and 1055 PPRs were predicted in the above four species, respectively, which were further mapped to chromosomes for a synteny analysis. Through an RNA-seq analysis, 86% (882) PPRs were expressed in flowering buds of upland cotton (G. hirsutum); however, only 11 and 6 were differentially expressed (DE) between restorer R and its near-isogenic (NI) B and between R and its NI A line, respectively. Another RNA-seq analysis identified the expression of only 54% (556) PPRs in 0 and 3day(s) post-anthesis (DPA) ovules and 24% (247) PPRs in 10 DPA fibers; however, only 59, 6, and 27 PPRs were DE in 0 and 3 DPA ovules, and 10 DPA fibers between two backcross inbred lines (BILs) with differing fiber length, respectively. Only 2 PPRs were DE between Xuzhou 142 and its fiberless and fuzzless mutant. Quantitative RT-PCR analysis confirmed the validity of the RNA-seq results for the gene expression pattern. Therefore, only a very small number of PPRs may be associated with fertility restoration of CMS and genetic differences in fiber initiation and elongation. These results lay a foundation for understanding the roles of PPR genes in cotton, and will be useful in the prioritization of candidate PPR gene functional validation for cotton CMS restoration and fiber development.

Mapping and genetic validation of a grain size QTL qGS7.1 in rice (Oryza sativa L.)

Grain size is a major determinant of grain weight, which is one of the components of rice yield. The objective o this study was to identify novel, and important quantitative trait loci (QTLs) for grain size and weight in rice. QTLs were mapped using a BC4F4 population including 192 backcross inbred lines (BILs) derived from a backcross between Xiaolijing (XLJ) and recombinant inbred lines (RILs). The mapping population was planted in both Lingshui (Hainan, 2015) and Fuyang (Zhejiang, 2016), with the short- and long-day conditions, respectively. A total of 10 QTLs for grain length, four for grain width, four for the ratio of grain length to width, and 11 for grain weight were detected in at least one environment and were distributed across 11 chromosomes. The phenotypic variance explained ranged from 6.76–25.68%, 14.30–34.03%, 5.28–26.50%, and 3.01–22.87% for grain length, grain width, the ratio of grain length to width, and thousand grain weight, respectively. Using the sequential residual heterozygotes (SeqRHs) method, qGS7.1, a QTL for grain size and weight, was mapped in a 3.2-Mb interval on chromosome 7. No QTLs about grain size and weight were reported in previous studies in this region, providing a good candidate for functional analysis and breeding utilization.

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.

Development of a drought stress-resistant rice restorer line through Oryza sativa–rufipogon hybridization

Restorer line F6 (Oryza sativa L. ssp. indica) has been widely used in hybrid rice breeding systems in southern China. However, line F6 is susceptible to drought stress, which restricts its utilization in many areas. Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) has strong drought stress resistance, but the molecular factors responsible for drought resistance in DXWR remain unknown. In this study, we used the combination of phenotypic selection and molecular marker-assisted selection (MAS) to improve the drought stress resistance of line F6 by introgression of qSDT12-2, a large effect drought stress-related quantitative trait locus identified in DXWR. Molecular MAS was carried out using linked marker RM1226, which is associated with qSDT12-2. Genomic background assessmentwas performed using 112 polymorphic markers. Finally, a stable drought stress-resistant backcross inbred line (BIL) was developed from a BC5F5 population, termed BIL627. Genetic constitution analysis revealed that the genome of BIL627 is almost identical (99.1%) to that of the restorer line F6. Further, BIL627 showed no yield penalty and no decrease in restorationability under normal conditions. Taken together, our findings reveal the intrinsic value of using genetic resources present in wild species of Oryza to improve undesirable traits found in cultivated rice.

Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population

BackgroundThe development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal.ResultsWe used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78–7.78 Mb (QBPH4.1) and 15.22–17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.ConclusionOn the one hand, HPs of OsLekRK2–3, OsSTPS2, and BPH32 determined broad-spectrum resistance to BPH among RH-derived BILs. On the other hand, in the JHN mutant population, BPH9 together with seven significant genes on chromosome 4 played a crucial role in BPH resistance.

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.

Mapping QTL forFusariumhead blight resistance in a tunisian-derived durum wheat population

Fusarium head blight (FHB) damage in durum wheat (Triticum turgidum L. var. durum Desf., turgidum) inflicted massive economic losses worldwide. Meanwhile, FHB resistant durum wheat germplasm is extremely limited. ‘Tunisian108’ is a newly identified tetraploid wheat with FHB resistance. However, genomic regions in ‘Tunisian108’ that significantly associated with FHB resistance are yet unclear. Therefore, a population of 171 backcross inbred lines (BC1F7) derived from a cross between ‘Tunisian108’ and a susceptible durum cultivar ‘Ben’ was characterized. Fusarium graminearum (R010, R1267, and R1322) was point inoculated (greenhouse) or spawn inoculated (field) in 2010 and 2011. Disease severity, Fusarium-damaged kernel (FDK) and mycotoxins were measured. Analysis of variance showed significant genotype and genotype by environment effect on all traits. Approximately 8% of the lines in field and 25% of the lines in greenhouse were more resistance than Tunisian108. A framework linkage map of 267 DArt plus 62 SSR markers was developed representing 239 unique loci and covering a total distance of 1887.6 cM. Composite interval mapping revealed nine QTL for FHB severity, four QTL for DON, and four QTL for FDK on seven chromosomes. Two novel QTL, Qfhb.ndsu-3BL and Qfhb.ndsu-2B, were identified for disease severity, explaining 11 and 6% of the phenotypic variation, respectively. Also, a QTL with large effect on severity and a QTL with negative effect on FDK on chromosome 5A were identified. Importantly, a novel region on chromosome 2B was identified with multiple FHB resistance. Validation on these QTL would facilitate the durum wheat resistance breeding.

Dissecting the quantitative variations of threshability in rice (<i>Oryza sativa</i> L.)

In rice, low threshability retains grains on the panicles especially in japonica rice ( O. sativa subsp. Japonica ) and high threshability makes it easier for harvesting in indica. The genetic mechanisms underlying moderate threshability in rice remain largely unclear. A set of reciprocal Backcross Inbred Lines BILs including 226 and 229 lines from indica rice ( O. sativa subsp. indica) and japonica rice (O. sativa subsp. japonica) backgrounds, respectively, and 262 recombinant inbred lines RILs developed from same cross between an indica, were adopted for testing threshability in two seasons. Percentages of dislodged grains were estimated at the maturity, harvesting and after sun drying. A total of 265 SNP markers developed based on sequencing and evenly distributed throughout the 12 chromosomes were used for genotyping assay. Inclusive composite interval mapping (ICIM) was used to dissect genomic regions and interactions affecting quantitative variation of threshability. A total of 13 QTLs were found to be conferring quantitative variations of threshability, which were distributed on all chromosomes. Two known major genes (QTLs) qSH1 and sh4 were also present. New additive QTLs, qThr1-a, qThr2, qThr3 qThr7, qThr8, qThr10, qThr11 and qThr12 were found as well. Twenty-four epistatics QTLs of which eight were common in both japonica and indica backgrounds were detected in two consecutive seasons. The overall threshability explained by all additive and interacting QTLs (R2) were 70% and 1 for indica, 15 and 8% for japonica and 17.4 and 10.6% for RIL backgrounds, respectively. Findings have preliminarily revealed a relatively complex mechanism underlying the quantitative variations of threshability in rice, which was controlled not only by major loci but also affected by epistasis and genetic background effects. Key words : epistasis, genetic background effect, quantitative variation, rice ( Oryza sativa L .), threshability

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.

A targeted QTL analysis for fiber length using a genetic population between two introgressed backcrossed inbred lines in upland cotton (Gossypium hirsutum)

Cotton fiber is the most important natural raw material for the textile industry, and fiber length (FL) is one of the most important traits in cotton. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for FL. In our study, two backcrossed inbred lines (BILs) were chosen as parents to construct a high-density genetic map in F2 which was used to fine map FL QTL in F2:3 population. The genetic map had a total size of 3462.8 cM, containing 9182 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing. Two FL related stable QTL were identified on two chromosomes (qFL-A08–1 on A08 and qFL-D03–1 on D03), and qFL-A08–1 was confirmed by a meta-analysis. Utilizing previously obtained RNA-seq data for the two BILs and qRT-PCR analysis, two candidate genes annotated as cytochrome b5 (CB5, Gh_A08G1729) and microtubule end-binding 1C (EB1C, Gh_D03G0232) that may regulate FL during the fiber elongation stage were identified. In addition, nine recombination hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of fiber elongation.

QTL Mapping of Seed Vigor of Backcross Inbred Lines Derived From Oryza longistaminata Under Artificial Aging.

Seed vigor is an important character of seed quality that promotes rice to germinate rapidly from soil and developing to a strong seedling, especially in the current rice direct-sowing production system. However, previous studies for seed vigor mainly concentrate in cultivars, and less reports involving in wild rice. In this study, 152 backcross inbred lines (BILs) derived from wild rice Oryza longistaminata were genotyped with re-sequencing technology, and QTLs for seed vigor related traits under normal and artificial aging treatment were analyzed. Totally, 36 QTLs were detected, of which, eight for germination potential (GP), 10 for germination rate (GR), 9 for seedling length (SL), and 9 for root length (RL). Among these, 14 novel QTLs were identified from O. longistaminata. Of which, six QTLs were related to germination, and eight related to seedling growth under aging stress. What’s more, the major QTLs q9SL1.1, q6SL1.1, and q3SL1.1 for seedling length were fallen in the same locus and fine-mapped an interval about 90 Kb. The major QTLs q9GR8.1 and q9GP8.1 related with germination were fine-mapped to an interval about 90 Kb. This work will provide us basis for breeding of high seed vigor rice in rice breeding programs and further cloning of these genes.

Selection of Transcripts Affecting Initial Growth Rate of Rice Backcrossed Inbred Lines Using RNA Sequencing Data.

Seedling growth is an important factor for direct seeding of rice. However, the genetic and transcriptomic factors involved in this process are largely unknown. In this study, transcripts affecting shoot weight were identified in rice (Oryza sativa L.) using RNA sequencing (RNA-Seq) data from 20 backcrossed inbred lines (BILs) and their parental cultivars. The selection frequency of the genes for the regression model was determined using repeated analysis of random subsets of the transcriptome. The qLTG3-1gene, controlling low-temperature germinability, and short grain 1 gene (SG1), known to decrease organ elongation, showed high frequency. The quantitative trait loci (QTLs) analysis performed for BILs revealed that qLTG3-1 was included in the QTLs for shoot weight but SG1 was not. No nucleotide polymorphisms were found in the coding region of SG1 in either of the parental cultivars. Quantitative real-time PCR showed that SG1 expression was negatively correlated with shoot weight for all 104 BILs analyzed in this study. Expression QTL (eQTLs) analysis showed an eQTL for SG1 expression located in the same region as the QTL for shoot weight. However, no eQTLs were detected on the same chromosome as SG1, suggesting that nucleotide polymorphisms around the gene do not affect its expression in analyzed growth stage. Overall, these results indicate that RNA-Seq is a useful tool for identifying transcripts that can be related to seedling growth rate.

Patterns of Transmission Ratio Distortion in Interspecific Lettuce Hybrids Reveal a Sex-Independent Gametophytic Barrier.

Interspecific crosses can result in progeny with reduced vitality or fertility due to genetic incompatibilities between species, a phenomenon known as hybrid incompatibility (HI). HI is often caused by a bias against deleterious allele combinations, which results in transmission ratio distortion (TRD). Here, we determined the genome-wide distribution of HI between wild lettuce, Lactuca saligna, and cultivated lettuce, L. sativa, in a set of backcross inbred lines (BILs) with single introgression segments from L. saligna introgressed into a L. sativa genetic background. Almost all BILs contained an introgression segment in a homozygous state except a few BILs, for which we were able to obtain only a single heterozygous introgression. Their inbred progenies displayed severe TRD with a bias toward the L. sativa allele and complete nontransmission of the homozygous L. saligna introgression, i.e., absolute HI. These HI might be caused by deleterious heterospecific allele combinations at two loci. We used an multilocus segregating interspecific F2 population to identify candidate conspecific loci that can nullify the HI in BILs. Segregation analysis of developed double-introgression progenies showed nullification of three HI and proved that these HI are explained by nuclear pairwise incompatibilities. One of these digenic HI showed 29% reduced seed set and its pattern of TRD pointed to a sex-independent gametophytic barrier. Namely, this HI was caused by complete nontransmission of one heterospecific allele combination at the haploid stage, surprisingly in both male and female gametophytes. Our study shows that two-locus incompatibility systems contribute to reproductive barriers among Lactuca species.

A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population.

Summary We present a complementary resource for trait fine‐mapping in tomato to those based on the intra‐specific cross between cultivated tomato and the wild tomato species Solanum pennellii, which have been extensively used for quantitative genetics in tomato over the last 20 years. The current population of backcross inbred lines (BILs) is composed of 107 lines derived after three backcrosses of progeny of the wild species Solanum neorickii (LA2133) and cultivated tomato (cultivar TA209) and is freely available to the scientific community. These S. neorickii BILs were genotyped using the 10K SolCAP single nucleotide polymorphism chip, and 3111 polymorphic markers were used to map recombination break points relative to the physical map of Solanum lycopersicum. The BILs harbor on average 4.3 introgressions per line, with a mean introgression length of 34.7 Mbp, allowing partitioning of the genome into 340 bins and thereby facilitating rapid trait mapping. We demonstrate the power of using this resource in comparison with archival data from the S. pennellii resources by carrying out metabolic quantitative trait locus analysis following gas chromatography–mass spectrometry on fruits harvested from the S. neorickii BILs. The metabolic candidate genes phenylalanine ammonia‐lyase and cystathionine gamma‐lyase were then tested and validated in F2 populations and via agroinfiltration‐based overexpression in order to exemplify the fidelity of this method in identifying the genes that drive tomato metabolic phenotypes.

A comparative analysis of small RNAs between two Upland cotton backcross inbred lines with different fiber length: Expression and distribution

The cotton fiber is the most important raw material for the textile industry and an ideal model system for studying cell elongation. However, the genetic variation of fiber elongation in relation to miRNA is poorly understood. A high-throughput comparative RNA-seq of two lines differing in fiber length (FL) from a backcross inbred line (BIL) population of G. hirsutum × G. barbadense revealed differentially expressed (DE) miRNAs and their targets in rapidly elongating fibers. A real-time quantitative PCR analysis was further performed to validate the results. A total of 463 (including 47 DE) miRNAs were identified, and seven DE miRNAs were co-localized with seven FL quantitative trait loci (QTL) identified in the G. hirsutum × G. barbadense population. Of 82 (including 21 DE) targets identified, nine (including one DE) were also co-localized with the seven FL QTL. The relationship between the allopolyploid and its diploid ancestral species with respect to miRNAs and their targets was also characterized. These results will facilitate the understanding of the molecular genetic mechanism of fiber elongation with regards to miRNAs in cotton.

Genetic enhancement of phosphorus starvation tolerance through marker assisted introgression of OsPSTOL1 gene in rice genotypes harbouring bacterial blight and blast resistance.

Phosphorus (P), an essential macronutrient, is a prerequisite for various plant-growth mechanisms including root establishment/development, early/late vegetative stage development and reproductive stage development. Rice (Oryza sativa) is very sensitive to P starvation. Most cultivated genotypes have poor tolerance levels to P deficiency and consequently the grain yield is severely affected by P starvation. Since P deficiency of soils is a major concern of rice production areas, it is necessary to develop new cultivars with enhanced P tolerance. This is also an expectation of farmers and the Agriculture ministry of southern states of India where rice cultivation is intensive. Our objective was to introgress the phosphorus starvation tolerance (OsPSTOL1) gene through marker-assisted backcross breeding (MABB) in to two intermediate genetic stocks of popular local-varieties namely, ASD 16 and ADT 43 which harbour bacterial blight and blast resistance (R) genes. To delve into the P starvation phenotypic effect, we have generated a set of four backcross inbred lines (BILs) with enhanced P starvation tolerance. The developed BILs showed altered root architecture pattern and greater root surface area with increased P uptake, confirming their adaptability to P deficient soil conditions. Further, a correlation between root traits and low/high P conditions indicates the function of introgressed OsPSTOL1 in BILs. The enhanced root characteristics, therefore, enabled the plants to access and effectively absorb available nutrients from soil. In summary, the unique features of the OsPSTOL1 BILs with bacterial blight and blast resistance can aid varietal development suitable for cultivation in P deficient soils.

Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato

To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci (mQTL) analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines (IL). To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a near-isogenic sub-IL population. We identified a putative lecithin:cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols (DAGs) and triacylglycerols (TAGs). Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. Taken together, our study extensively characterized the genetic architecture of lipophilic compounds in tomato and demonstrated at molecular level that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.