Study of polyembryony and development of molecular markers for identification of zygotic and nucellar seedlings in Khasi mandarin (Citrus reticulata Blanco)

The objective of this work was to evaluate the occurrence of polyembryonic seedlings and other morphological parameters in Khasi mandarin during three harvest years and to identify zygotic (sexual) seedlings from nucellar (asexual) ones grown under in-vitro conditions using molecular markers. Embryos from 27 polyembryonic and 7 monoembryonic seeds of Khasi mandarin were grown in-vitro. DNA from seedlings and mother parent was analyzed using 16 ISSR and 5 RAPD primers, of which 4 ISSR and a set of 3 RAPD primers were effective to identify zygotic or nucellar origin of the seedlings. In-vitro culture enables maximum embryos of each seed to grow, favouring the origin of seedlings to be identified as zygotic. Among 69 tested individuals, 37 zygotic and 32 nucellar seedlings were recognized. In polyembryonic and monoembryonic seeds, 59.6% and 42.8% of the seedlings, respectively, have the sexual origin. Morphological characteristics of seeds and the seedlings generated varied significantly and were not correlated with polyembryony except for the clutch size and the number of branches. Polyembryonic seeds in the cultivar are high, ranging from 50.0%, 55.5% to 83.3% over three harvest years with more clutch size and the possibility of obtaining zygotic plants from them is high. In polyembryonic seeds not all zygotic seedlings were produced by small embryos located at the micropyle. Identification of zygotic seedlings by ISSR and RAPD markers in Khasi mandarin cultivar is efficient and reliable at an early developmental stage

Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives

Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species

Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example

© The Author(s) 2017 This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/ genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.Peer reviewedFinal Published versio

QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: importance of recurrent selection backcross scheme for the identification of 'true' QTL

Seed glucosinolate content in Brassica juncea is a complex quantitative trait. A recurrent selection backcross (RSB) method with a doubled haploid (DH) generation interspersing backcross generations was used for the introgression of low glucosinolate alleles from an east European gene pool B. juncea line, Heera into an Indian gene pool variety, Varuna. Phenotypic comparisons among the DH populations derived from early to advanced backcrosses revealed a shift in the mean values for various glucosinolates with the advancement of backcrossing, indicating a change in the selective values of the alleles with change in the genetic background due to the existence of epistasis and context dependencies. QTL mapping for various seed glucosinolates from early (F<SUB>1</SUB>DH) and advanced generation (BC<SUB>4</SUB>DH) populations confirmed the presence of epistasis and context dependency. The common QTL detected in both F<SUB>1</SUB>DH and BC<SUB>4</SUB>DH changed their R<SUP>2</SUP> values from the former to the later generation. Some of the QTL detected in the F<SUB>1</SUB>DH became irrelevant in the BC<SUB>4</SUB>DH population. Further, new QTL were detected in the BC<SUB>4</SUB>DH population for various glucosinolates. A validation study on a population of low glucosinolate DH lines derived from all the backcross generations of the RSB breeding programme revealed that the QTL detected in BC<SUB>4</SUB>DH were the 'true' QTL. Using glucosinolate as an example, the study provides strong evidence for the importance of the RSB method for the identification of the 'true' QTL which would be significant for marker assisted introgression of a complex quantitative trait whose expression is influenced by epistatic interactions

Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas

Quantitative trait loci (QTL) analysis of yield influencing traits was carried out in Brassica juncea (AABB) using a doubled haploid (DH) mapping population of 123 lines derived from a cross between Varuna (a line representing the Indian gene pool) and Heera (representing the east European gene pool) to identify potentially useful alleles from both the parents. The existing AFLP based map of B. juncea was further saturated with RFLP and SSR markers which led to the identification of the linkage groups belonging to the A (B. rapa) and B (B. nigra) genome components of B. juncea. For QTL dissection, the DH lines were evaluated at three different environments and phenotyped for 12 quantitative traits. A total of 65 QTL spread over 13 linkage groups (LG) were identified from the three environments. QTL analysis showed that the A genome has contributed more than the B genome to productivity (68% of the total QTL detected) suggesting a more prominent role of the A genome towards domestication of this crop. The east European line, Heera, carried favorable alleles for 42% of the detected QTL and the remaining 58% were in the Indian gene pool line, Varuna. We observed clustering of major QTL in a few linkage groups, particularly in J7 and J10 of the A genome, with QTL of different traits having agronomically antagonistic allelic effects co-mapping to the same genetic interval. QTL analysis also identified some well-separated QTL which could be readily transferred between the two pools. Based on the QTL analysis, we propose that improvement in yield could be achieved more readily by heterosis breeding rather than by pure line breeding