Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Drought is a major abiotic constraint for rice production worldwide. The quantitative trait loci (QTLs) for drought tolerance traits identified in earlier studies have large confidence intervals due to low density linkage maps. Further, these studies largely focused on the above ground traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative growth stage using a genotyping by sequencing (GBS) based saturated SNP linkage map. A recombinant inbred line (RIL) population from a cross between Cocodrie and N-22 was evaluated for eight morphological traits under drought stress. Drought was imposed to plants grown in 75 cm long plastic pots at the vegetative growth stage. Using a saturated SNP linkage map, 14 additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. Majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated condition. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL confidence intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. Another important gene, Brevis radix, present in the root length QTL region, was known to modulate root growth through cell proliferation and elongation. The candidate genes and the QTL information will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.     

Effect of maturity and temperature on breeding for mid-oleic soybean lines under the high heat conditions of the Mississippi Delta,USA

Soybean (Glycine max (L) Merr.) seed is an important source of oil for human consumption. Increasing the percentage of oleic acid in soybean seed oil is an important breeding objective because increasing the oleic acid content improves the oxidative stability of the oil. Extensive literature shows that temperature during seed-fill is positively correlated with the content of oleic acid in soybeans. In addition, it was shown that a maturity QTL was linked to an oleic acid QTL. The Mississippi Delta in the USA is a hot environment where soybean harvest begins in August, which is the hottest part of the season. The purpose of this research was to determine the possibility of developing both early- and late-maturing lines with consistent >?50% oleic acid content in Mississippi. We selected early and late segregants from three genetically different breeding populations also segregating for mid-oleic acid derived from crosses to germplasm N98-4445A, a non-transgenic freely available line with >?50% oleic acid. The selected lines were grown in 2 years in three trials at Stoneville, MS. Results indicated that no late-maturing lines (MG V) met the targeted mid-oleic acid level, whereas MG III and early MG IV lines with oleic acid over 50% were obtained. No maturity-alone effect on oleic acid content was observed, due to the bias of the strong negative correlation between maturity date and mean temperature during seed-fill. This study demonstrated that breeders can effectively develop early soybeans with oleic acid levels greater than 50% for the midsouthern USA.     

Molecular and comparative mapping for heading date and plant height in oat

Selection of oat genotypes combining earliness and short plant height could stimulate oat cultivation worldwide. However, the mechanisms involved with the genetic control of heading date and plant height traits are not fully understood to date. This study aimed to identify genomic regions controlling heading date and plant height in two hulled by naked oat populations and to compare these genomic regions with that of other grass species. Recombinant inbred lines of each population and their parents were genotyped by a 6 K BeadChip Illumina Infinium array and assessed for heading date and plant height in two sowing dates. The quantitative trait loci (QTL) affecting these traits were detected by simple interval mapping. The two oat populations showed different genetic mechanisms controlling heading date. A major QTL was identified in one of the populations, mapped into the ‘Mrg33’ consensus linkage group from the current oat map. Two other QTL were detected into the ‘Mrg02’ and ‘Mrg24’ groups, in the second population. On the other hand, both populations presented the same genomic region controlling plant height. Six SNP markers, mapping on the same linkage group within each population, were associated with the trait, regardless the sowing date, explaining more than 20% of the phenotypic variation. Five of these six markers were mapped into three different linkage groups on the oat consensus map. Genomic regions associated with heading date and plant height in oat seem to be conserved in Oryza sativa L. and Brachypodium distachyon. Our results provide valuable information for marker-assisted selection in oats, allowing selection for earliness and plant height on early segregating generations.     

Introgression of <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. into Upland cotton germplasm RMBUP-C4S1

Gossypium barbadense L. cotton has significantly better fiber quality than Upland cotton (G. hirsutum L.); however, yield and environmental adaptation of G. barbadense is not as wide as Upland. Most cotton in the world is planted to Upland cultivars. Many attempts have been made, over a considerable number of years, to introgress fiber quality alleles from G. barbadense into Upland. However, introgression barriers, primarily in the form of interspecific incompatibility, have limited these traditional approaches. The use of chromosome substitution lines (CSL) as a bridge should provide a more efficient way to introgress alleles from G. barbadense into Upland. We crossed 18 G. barbadense CSL to three cultivars and developed a random mated population. After five cycles of random mating followed by one generation of self-pollination to increase the seed supply, we grew the random mated population and used 139 G. barbadense chromosome specific SSR markers to assess a random sample of 96 plants for introgression. We recovered 121 of 139 marker loci among the 96 plants. The distribution of the G. barbadense alleles ranged from 10 to 28 alleles in each plant. Among the 96 plants we found individual plants with marker loci from 6 to 14 chromosomes or chromosome arms. Identity by descent showed little relatedness among plants and no population structure was indicated by a heat map. Using CSL we were able to develop a mostly Upland random mated population with considerable introgression of G. barbadense alleles which should be useful for breeding.     

Evaluation of a multi-parent advanced generation inter-cross (MAGIC) introgressed line population for Verticillium wilt resistance in Upland cotton

Verticillium wilt (VW, caused by Verticillium dahliae Kleb) is a destructive fungal soil-borne disease in Upland cotton (Gossypium hirsutum L.). High levels of VW resistance can be transferred into Upland from Pima cotton (G. barbadense L.) through interspecific introgression breeding. In this greenhouse study, VW resistance was evaluated in a multi-parent advanced generation inter-cross (MAGIC) introgressed line (IL) population, derived from a random mated Barbadense Upland population with five generations of intermating (called RMBUP-C4) between three Upland cotton cultivars and 18 CS-B Upland lines each carrying a pair of G. barbadense chromosome or arm in the TM-1 background. The objectives of this study were to, (1) evaluate VW resistance of 530 MAGIC ILs in the greenhouse; and (2) to identify lines with VW resistance in the MAGIC population based on a total of three replicated greenhouse tests. Approximately 8 plants for each line in each replicate were grown and screened for VW resistance using three parameters i.e., disease leaf severity rating, percentage defoliated leaves, and percentage infected plants, with a total of ~?25,190 plants evaluated. A correlation analysis indicated that the three parameters were significantly and positively correlated with one another in each test. The disease leaf severity rating was the best parameter to assess VW resistance due to its relatively low coefficient of variation and its higher resolution to differentiate resistant genotypes from susceptible ones. Of the 530 genotypes, 5 showed resistance to VW, namely, NMIL348, NMIL518, NMIL405, NMIL290, NMIL307 and had higher levels of resistance to VW with mean disease leaf severity ratings, percentage of defoliated leaves, and percentage of infected plants across three tests ranging from 0.58–1.46, 9.46–26.74, and 25–95%, respectively. These lines can be used as parental lines to improve VW resistance in cotton breeding programs.     

Genetic variability of faba bean genotypes for chocolate spot (<Emphasis Type="Italic">Botrytis fabae</Emphasis>) resistance and yield

Faba bean (Vicia faba L.) has high utility as a food and soil fertility improving crop. One of the major fungal pathogens of faba bean is Botrytis fabae, the causative agent of chocolate spot. The disease affects significantly the leaf, stem, pod and seed of faba bean compromise its productivity in the smallholder farming sector. Nonetheless, there are limited resistant/tolerant faba bean varieties available and disease control technology options. Therefore, it was prudent to evaluate faba bean landraces for chocolate spot resistance. Fifty landraces together with ten improved varieties were evaluated both in the field and in the greenhouse under natural and artificial inoculation with previously selected aggressive Botrytis fabae isolate (Iso-016) from West Gojjam, in Ethiopia. There were highly significant differences (p?<?0.001) among the landraces for reaction to the disease and agronomic traits. Significant positive correlation was recorded between reaction of genotypes in the field and greenhouse disease data. The overall mean disease epidemics varied from 92.5 to 697.5 for the area under disease progress curve (AUDPC). The highest level of resistance was found in the ICARDA lines, ILB-4726, ILB-938 and BPL-710. Of all 18 landrace collections displayed significantly lower disease reaction than the susceptible check. However the resistance was moderate. The selected eighteen landraces will be recommended for use in breeding for chocolate resistance. Overall, resistance was highly heritable, suggesting that phenotypic selection can be exploited to improve chocolate spot resistance in faba bean varieties.     

Broadening the genetic base of <Emphasis Type="Italic">Brassica napus</Emphasis> canola by interspecific crosses with different variants of <Emphasis Type="Italic">B. oleracea</Emphasis>

Broadening the genetic base of the C genome of Brassica napus canola by use of B. oleracea is important. In this study, the prospect of developing B. napus canola lines from B. napus?×?B. oleracea var. alboglabra, botrytis, italica and capitata crosses and the effect of backcrossing the F₁’s to B. napus were investigated. The efficiency of the production of the F₁’s varied depending on the B. oleracea variant used in the cross. Fertility of the F₁ plants was low—produced, on average, about 0.7 F₂ seeds per self-pollination and similar number of BC₁ seeds on backcrossing to B. napus. The F₃ population showed greater fertility than the BC₁F₂; however, this difference diminished with the advancement of generation. The advanced generation populations, whether derived from F₂ or BC₁, showed similar fertility and produced similar size silique with similar number of seeds per silique. Progeny of all F₁’s and BC₁’s stabilized into B. napus, although B. oleracea plant was expected, especially in the progeny of F₁ (ACC) owing to elimination of the A chromosomes during meiosis. Segregation distortion for erucic acid alleles occurred in both F₂ and BC₁ resulting significantly fewer zero-erucic plants than expected; however, plants with?≤?15% erucic acid frequently yielded zero-erucic progeny. No consistent correlation between parent and progeny generation was found for seed glucosinolate content; however, selection for this trait was effective and B. napus canola lines were obtained from all crosses. Silique length showed positive correlation with seed set; the advanced generation populations, whether derived from F₂ or BC₁, were similar for these traits. SSR marker analysis showed that genetically diverse canola lines can be developed by using different variants of B. oleracea in B. napus?×?B. oleracea interspecific crosses.     

Morph-physiological responses of cotton interspecific chromosome substitution lines to low temperature and drought stresses

Limited knowledge about genetic and physiological traits associated with drought and low temperature stresses and narrow genetic diversity in Upland cotton (Gossypium hirsutum L.) are serious impediments in its genetic improvement. The objectives of this research were to determine the genetic and physiological traits associated with drought and low temperature effects and to identify chromosomal effects on these traits using chromosome substitution (CS) lines from three alien species of Gossypium, G. barbadense, G. tomentosum, and G. mustelinum, respectively. Two experiments were conducted to study low temperature and drought stress effects during seedling emergence and early growth stages in 21 cotton CS-lines with parent, Texas Marker (TM)-1. In Experiment I, plants were grown at optimum (30/22 °C) and low (22/14 °C) temperature conditions under optimum water and nutrient conditions. In Experiment II, plants were grown at optimum water (soil moisture content of 0.167 m³ m^?3) and in drought (soil moisture content 0.105 m³ m^?3) conditions under optimum temperature conditions. Above- and below-ground growth traits including several root traits of the CS lines were assessed at 25 days after sowing. The findings suggest which substituted chromosome or chromosome segment from the alien species likely harbors one or more genes for higher and lower tolerance to low temperature, respectively. CS-T04 and CSB08sh showed higher and lower tolerance to low temperature, respectively and CS-T04 and CS-B22sh showed higher and lower tolerance, respectively, to drought. CS lines are valuable analytical tool and useful genetic resources for targeted exploitation of beneficial genes for drought and low temperature stresses in Upland cotton.     

Identification of genetic sources with attenuated <Emphasis Type="Italic">Tomato chlorosis virus</Emphasis>-induced symptoms in <Emphasis Type="Italic">Solanum</Emphasis> (section <Emphasis Type="Italic">Lycopersicon</Emphasis>) germplasm

The whitefly-transmitted Tomato chlorosis virus (ToCV) (genus Crinivirus) is associated with yield and quality losses in field and greenhouse-grown tomatoes (Solanum lycopersicum) in South America. Therefore, the search for sources of ToCV resistance/tolerance is a major breeding priority for this region. A germplasm of 33 Solanum (Lycopersicon) accessions (comprising cultivated and wild species) was evaluated for ToCV reaction in multi-year assays conducted under natural and experimental whitefly vector exposure in Uruguay and Brazil. Reaction to ToCV was assessed employing a symptom severity scale and systemic virus infection was evaluated via RT-PCR and/or molecular hybridization assays. A subgroup of accessions was also evaluated for whitefly reaction in two free-choice bioassays carried out in Uruguay (with Trialeurodes vaporariorum) and Brazil (with Bemisia tabaci Middle-East-Asia-Minor1—MEAM1?=?biotype B). The most stable sources of ToCV tolerance were identified in Solanum habrochaites PI 127827 (mild symptoms and low viral titers) and S. lycopersicum ‘LT05’ (mild symptoms but with high viral titers). These two accessions were efficiently colonized by both whitefly species, thus excluding the potential involvement of vector-resistance mechanisms. Other promising breeding sources were Solanum peruvianum (sensu lato) ‘CGO 6711’ (mild symptoms and low virus titers), Solanum chilense LA1967 (mild symptoms, but with high levels of B. tabaci MEAM1 oviposition) and Solanum pennellii LA0716 (intermediate symptoms and low level of B. tabaci MEAM1 oviposition). Additional studies are necessary to elucidate the genetic basis of the tolerance/resistance identified in this set of Solanum (Lycopersicon) accessions.     

Effectiveness of early-generation testing applied to upland rice breeding

A plant breeding program is a long-term investment. Therefore, periodic assessment of the effectiveness of a breeding strategy is essential to maximize genetic gains per unit of time and resource invested. In this work, we assessed the effectiveness of the early-generation testing (EGT) approach used in the upland rice (Oryza sativa L.) breeding program at Embrapa (Brazilian Agricultural Research Corporation), Brazil, estimating the genetic progress achieved for three traits in two distinct phases, spanning 15 years. In the first phase (from 2003 to 2010), it was used the bulk method within F₃ progenies with prior testing of F₂ crosses, while in the second phase (from 2010 to 2017), it was used the bulk method within F₂ progenies. The dataset comprised 70 yield trials, involving 1884 F_3:5 progenies (phase I) and 925 F_2:4 progenies (phase II) from an elite population, and 10 check cultivars, evaluated for grain yield (GY), plant height (PH) and days to flowering (DTF). For estimating the genetic gain, we adapted a generalized linear regression method to compute bi-segmented linear regression coefficients. Desirable genetic gains were achieved only for GY in both phases of the breeding program, with 78.75 kg ha^?1 year^?1 (2.68%) in the first phase, and 53.78 kg ha^?1 year^?1 (1.54%) in the second phase. These results show the effectiveness of EGT, especially via bulk method within F₃ progenies with prior testing of F₂ crosses, applied to upland rice breeding. Some refinements are discussed in the method to make it more cost-effective and more efficient in achieving genetic gains.